diff --git a/src/main/agent-trust-presets.test.ts b/src/main/agent-trust-presets.test.ts
index 4b4575fd6c2..41b3962d4e5 100644
--- a/src/main/agent-trust-presets.test.ts
+++ b/src/main/agent-trust-presets.test.ts
@@ -13,9 +13,21 @@ import { join } from 'node:path'
 import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest'
 
 const testState = {
-  fakeHomeDir: ''
+  fakeHomeDir: '',
+  userDataDir: ''
 }
 
+vi.mock('electron', () => ({
+  app: {
+    getPath: (name: string) => {
+      if (name === 'userData') {
+        return testState.userDataDir
+      }
+      throw new Error(`unexpected app.getPath(${name})`)
+    }
+  }
+}))
+
 vi.mock('node:os', async () => {
   // eslint-disable-next-line @typescript-eslint/consistent-type-imports -- vi.importActual requires inline import()
   const actual = await vi.importActual<typeof import('node:os')>('node:os')
@@ -30,11 +42,14 @@ const { markCodexProjectTrusted, markCopilotFolderTrusted, markCursorWorkspaceTr
 
 beforeEach(() => {
   testState.fakeHomeDir = mkdtempSync(join(tmpdir(), 'orca-trust-presets-'))
+  testState.userDataDir = mkdtempSync(join(tmpdir(), 'orca-trust-presets-user-data-'))
 })
 
 afterEach(() => {
   rmSync(testState.fakeHomeDir, { recursive: true, force: true })
+  rmSync(testState.userDataDir, { recursive: true, force: true })
   testState.fakeHomeDir = ''
+  testState.userDataDir = ''
 })
 
 describe('markCursorWorkspaceTrusted', () => {
@@ -119,10 +134,20 @@ describe('markCodexProjectTrusted', () => {
       const realpath = realpathSync(workspace)
       markCodexProjectTrusted(workspace)
       const configPath = join(testState.fakeHomeDir, '.codex', 'config.toml')
+      const runtimeConfigPath = join(
+        testState.userDataDir,
+        'codex-runtime-home',
+        'home',
+        'config.toml'
+      )
       expect(existsSync(configPath)).toBe(true)
+      expect(existsSync(runtimeConfigPath)).toBe(true)
       const written = readFileSync(configPath, 'utf-8')
+      const runtimeWritten = readFileSync(runtimeConfigPath, 'utf-8')
       expect(written).toContain(`[projects."${escapeTomlBasicString(realpath)}"]`)
       expect(written).toContain('trust_level = "trusted"')
+      expect(runtimeWritten).toContain(`[projects."${escapeTomlBasicString(realpath)}"]`)
+      expect(runtimeWritten).toContain('trust_level = "trusted"')
     } finally {
       rmSync(workspace, { recursive: true, force: true })
     }
@@ -133,7 +158,9 @@ describe('markCodexProjectTrusted', () => {
     const realpath = realpathSync(workspace)
     try {
       const codexDir = join(testState.fakeHomeDir, '.codex')
+      const runtimeCodexDir = join(testState.userDataDir, 'codex-runtime-home', 'home')
       mkdirSync(codexDir, { recursive: true })
+      mkdirSync(runtimeCodexDir, { recursive: true })
       writeFileSync(
         join(codexDir, 'config.toml'),
         [
@@ -146,14 +173,31 @@ describe('markCodexProjectTrusted', () => {
         ].join('\n'),
         'utf-8'
       )
+      writeFileSync(
+        join(runtimeCodexDir, 'config.toml'),
+        [
+          'sandbox_mode = "workspace-write"',
+          '',
+          `[projects."${escapeTomlBasicString(realpath)}"]`,
+          'notes = "keep-runtime"',
+          'trust_level = "untrusted"',
+          ''
+        ].join('\n'),
+        'utf-8'
+      )
 
       markCodexProjectTrusted(workspace)
 
       const written = readFileSync(join(codexDir, 'config.toml'), 'utf-8')
+      const runtimeWritten = readFileSync(join(runtimeCodexDir, 'config.toml'), 'utf-8')
       expect(written).toContain('model = "gpt-5.5"')
       expect(written).toContain('notes = "keep"')
       expect(written).toContain('trust_level = "trusted"')
       expect(written).not.toContain('trust_level = "untrusted"')
+      expect(runtimeWritten).toContain('sandbox_mode = "workspace-write"')
+      expect(runtimeWritten).toContain('notes = "keep-runtime"')
+      expect(runtimeWritten).toContain('trust_level = "trusted"')
+      expect(runtimeWritten).not.toContain('trust_level = "untrusted"')
     } finally {
       rmSync(workspace, { recursive: true, force: true })
     }
diff --git a/src/main/agent-trust-presets.ts b/src/main/agent-trust-presets.ts
index f71ed9e4408..56220d41f4a 100644
--- a/src/main/agent-trust-presets.ts
+++ b/src/main/agent-trust-presets.ts
@@ -2,6 +2,7 @@ import { existsSync, mkdirSync, readFileSync, realpathSync } from 'node:fs'
 import { homedir } from 'node:os'
 import { join } from 'node:path'
 import { writeFileAtomically } from './codex-accounts/fs-utils'
+import { getOrcaManagedCodexHomePath } from './codex/codex-home-paths'
 import { upsertProjectTrustLevel } from './codex/config-toml-trust'
 
 /**
@@ -109,6 +110,9 @@ export function markCodexProjectTrusted(workspacePath: string): void {
   const absPath = canonicalize(workspacePath)
   const configPath = join(homedir(), '.codex', 'config.toml')
   upsertProjectTrustLevel(configPath, absPath, 'trusted')
+  // Why: Orca-launched Codex runs with an Orca-owned CODEX_HOME, so the trust
+  // preset must also update the runtime config Codex will actually read.
+  upsertProjectTrustLevel(join(getOrcaManagedCodexHomePath(), 'config.toml'), absPath, 'trusted')
 }
 
 function canonicalize(p: string): string {
diff --git a/src/main/codex-accounts/runtime-home-service.test.ts b/src/main/codex-accounts/runtime-home-service.test.ts
index d820830af8c..154b3358f6e 100644
--- a/src/main/codex-accounts/runtime-home-service.test.ts
+++ b/src/main/codex-accounts/runtime-home-service.test.ts
@@ -118,6 +118,22 @@ function createSettings(overrides: Partial<GlobalSettings> = {}): GlobalSettings
   }
 }
 
+function getSystemCodexHomePath(): string {
+  return join(testState.fakeHomeDir, '.codex')
+}
+
+function getSystemCodexAuthPath(): string {
+  return join(getSystemCodexHomePath(), 'auth.json')
+}
+
+function getRuntimeCodexHomePath(): string {
+  return join(testState.userDataDir, 'codex-runtime-home', 'home')
+}
+
+function getRuntimeCodexAuthPath(): string {
+  return join(getRuntimeCodexHomePath(), 'auth.json')
+}
+
 function createStore(settings: GlobalSettings) {
   return {
     getSettings: vi.fn(() => settings),
@@ -182,7 +198,8 @@ describe('CodexRuntimeHomeService', () => {
     vi.clearAllMocks()
     testState.userDataDir = mkdtempSync(join(tmpdir(), 'orca-runtime-home-'))
     testState.fakeHomeDir = mkdtempSync(join(tmpdir(), 'orca-codex-home-'))
-    mkdirSync(join(testState.fakeHomeDir, '.codex'), { recursive: true })
+    mkdirSync(getSystemCodexHomePath(), { recursive: true })
+    mkdirSync(getRuntimeCodexHomePath(), { recursive: true })
   })
 
   afterEach(() => {
@@ -191,8 +208,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('captures the existing ~/.codex auth as the system-default snapshot', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
-    writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system"}\n', 'utf-8')
     const store = createStore(createSettings())
 
     const { CodexRuntimeHomeService } = await import('./runtime-home-service')
@@ -209,9 +225,9 @@ describe('CodexRuntimeHomeService', () => {
     }
   })
 
-  it('materializes the active managed account auth into ~/.codex on startup', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
-    writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
+  it('materializes the active managed account auth into the runtime home on startup', async () => {
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system"}\n', 'utf-8')
     const managedHomePath = createManagedAuth(
       testState.userDataDir,
       'account-1',
@@ -246,8 +262,8 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('restores the system-default snapshot when no managed account is selected', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
-    writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system"}\n', 'utf-8')
     const managedHomePath = createManagedAuth(
       testState.userDataDir,
       'account-1',
@@ -284,7 +300,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('removes runtime auth when restoring a no-login system default', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     const managedHomePath = createManagedAuth(
       testState.userDataDir,
       'account-1',
@@ -320,7 +336,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('removes runtime auth when deselecting with a missing system-default snapshot', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     const managedAuth = createCodexAuthJson('user@example.com', 'acct-1', 'managed')
     writeFileSync(runtimeAuthPath, managedAuth, 'utf-8')
     const managedHomePath = createManagedAuth(testState.userDataDir, 'account-1', managedAuth)
@@ -351,9 +367,9 @@ describe('CodexRuntimeHomeService', () => {
     expect(existsSync(runtimeAuthPath)).toBe(false)
   })
 
-  it('removes runtime auth when deselecting with a corrupt system-default snapshot', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
-    writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
+  it('repairs a corrupt system-default snapshot from the live ~/.codex auth on deselect', async () => {
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system"}\n', 'utf-8')
     const managedAuth = createCodexAuthJson('user@example.com', 'acct-1', 'managed')
     const managedHomePath = createManagedAuth(testState.userDataDir, 'account-1', managedAuth)
     const settings = createSettings({
@@ -373,7 +389,6 @@ describe('CodexRuntimeHomeService', () => {
       activeCodexManagedAccountId: null
     })
     const store = createStore(settings)
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => {})
 
     const { CodexRuntimeHomeService } = await import('./runtime-home-service')
     const service = new CodexRuntimeHomeService(store as never)
@@ -389,15 +404,15 @@ describe('CodexRuntimeHomeService', () => {
     settings.activeCodexManagedAccountId = null
     service.syncForCurrentSelection()
 
-    expect(existsSync(runtimeAuthPath)).toBe(false)
-    expect(existsSync(snapshotPath)).toBe(false)
-    expect(warnSpy).toHaveBeenCalledWith(
-      '[codex-runtime-home] Ignoring invalid system-default auth snapshot'
-    )
+    expect(readFileSync(runtimeAuthPath, 'utf-8')).toBe('{"account":"system"}\n')
+    expect(existsSync(snapshotPath)).toBe(true)
+    expect(JSON.parse(readFileSync(snapshotPath, 'utf-8'))).toEqual({
+      authJson: '{"account":"system"}\n'
+    })
   })
 
   it('clears an invalid active account selection and removes untrusted runtime auth', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const missingManagedHomePath = join(
       testState.userDataDir,
@@ -433,7 +448,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('clears an unknown active account id and removes untrusted runtime auth', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"stale-managed"}\n', 'utf-8')
     const settings = createSettings({
       activeCodexManagedAccountId: 'missing-account'
@@ -447,18 +462,18 @@ describe('CodexRuntimeHomeService', () => {
     expect(existsSync(runtimeAuthPath)).toBe(false)
   })
 
-  it('returns ~/.codex for Codex launch and rate-limit preparation', async () => {
+  it('returns the Orca-managed runtime home for Codex launch and rate-limit preparation', async () => {
     const store = createStore(createSettings())
     const { CodexRuntimeHomeService } = await import('./runtime-home-service')
     const service = new CodexRuntimeHomeService(store as never)
 
-    expect(service.prepareForCodexLaunch()).toBe(join(testState.fakeHomeDir, '.codex'))
-    expect(service.prepareForRateLimitFetch()).toBe(join(testState.fakeHomeDir, '.codex'))
-    expect(existsSync(join(testState.fakeHomeDir, '.codex'))).toBe(true)
+    expect(service.prepareForCodexLaunch()).toBe(getRuntimeCodexHomePath())
+    expect(service.prepareForRateLimitFetch()).toBe(getRuntimeCodexHomePath())
+    expect(existsSync(getRuntimeCodexHomePath())).toBe(true)
   })
 
   it('does not overwrite auth.json when no managed account was ever active', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"original"}\n', 'utf-8')
     const store = createStore(createSettings())
 
@@ -471,9 +486,151 @@ describe('CodexRuntimeHomeService', () => {
     expect(readFileSync(runtimeAuthPath, 'utf-8')).toBe('{"account":"external-switch"}\n')
   })
 
-  it('does not overwrite auth.json after deselection + external change', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
-    writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
+  it('refreshes the runtime auth when the system-default auth changes later', async () => {
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system-1"}\n', 'utf-8')
+    const store = createStore(createSettings())
+
+    const { CodexRuntimeHomeService } = await import('./runtime-home-service')
+    const service = new CodexRuntimeHomeService(store as never)
+
+    expect(readFileSync(runtimeAuthPath, 'utf-8')).toBe('{"account":"system-1"}\n')
+
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system-2"}\n', 'utf-8')
+    service.syncForCurrentSelection()
+
+    expect(readFileSync(runtimeAuthPath, 'utf-8')).toBe('{"account":"system-2"}\n')
+  })
+
+  it('reads back system-default token refreshes from runtime auth', async () => {
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system-old"}\n', 'utf-8')
+    const store = createStore(createSettings())
+
+    const { CodexRuntimeHomeService } = await import('./runtime-home-service')
+    const service = new CodexRuntimeHomeService(store as never)
+
+    writeFileSync(runtimeAuthPath, '{"account":"system-refreshed"}\n', 'utf-8')
+    service.syncForCurrentSelection()
+
+    expect(readFileSync(getSystemCodexAuthPath(), 'utf-8')).toBe('{"account":"system-refreshed"}\n')
+    expect(readFileSync(runtimeAuthPath, 'utf-8')).toBe('{"account":"system-refreshed"}\n')
+    expect(
+      JSON.parse(
+        readFileSync(
+          join(testState.userDataDir, 'codex-runtime-home', 'system-default-auth.json'),
+          'utf-8'
+        )
+      )
+    ).toEqual({ authJson: '{"account":"system-refreshed"}\n' })
+  })
+
+  it('reads back system-default token refreshes after restart when the snapshot proves the baseline', async () => {
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system-old"}\n', 'utf-8')
+    const store = createStore(createSettings())
+
+    const { CodexRuntimeHomeService } = await import('./runtime-home-service')
+    new CodexRuntimeHomeService(store as never)
+
+    writeFileSync(runtimeAuthPath, '{"account":"system-refreshed"}\n', 'utf-8')
+    const restartedService = new CodexRuntimeHomeService(store as never)
+    restartedService.syncForCurrentSelection()
+
+    expect(readFileSync(getSystemCodexAuthPath(), 'utf-8')).toBe('{"account":"system-refreshed"}\n')
+    expect(readFileSync(runtimeAuthPath, 'utf-8')).toBe('{"account":"system-refreshed"}\n')
+  })
+
+  it('keeps a local runtime logout when the system-default auth still exists', async () => {
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system"}\n', 'utf-8')
+    const store = createStore(createSettings())
+
+    const { CodexRuntimeHomeService } = await import('./runtime-home-service')
+    const service = new CodexRuntimeHomeService(store as never)
+
+    rmSync(runtimeAuthPath, { force: true })
+    service.syncForCurrentSelection()
+
+    expect(existsSync(runtimeAuthPath)).toBe(false)
+  })
+
+  it('keeps a local runtime logout after restart when the system-default auth still exists', async () => {
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system"}\n', 'utf-8')
+    const settings = createSettings()
+    const store = createStore(settings)
+
+    const { CodexRuntimeHomeService } = await import('./runtime-home-service')
+    const service = new CodexRuntimeHomeService(store as never)
+
+    rmSync(runtimeAuthPath, { force: true })
+    service.syncForCurrentSelection()
+    new CodexRuntimeHomeService(store as never)
+
+    expect(existsSync(runtimeAuthPath)).toBe(false)
+    expect(
+      existsSync(
+        join(testState.userDataDir, 'codex-runtime-home', 'system-default-runtime-logout.json')
+      )
+    ).toBe(true)
+  })
+
+  it('mirrors a fresh external system-default login after a persisted local runtime logout', async () => {
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system-old"}\n', 'utf-8')
+    const settings = createSettings()
+    const store = createStore(settings)
+
+    const { CodexRuntimeHomeService } = await import('./runtime-home-service')
+    const service = new CodexRuntimeHomeService(store as never)
+
+    rmSync(runtimeAuthPath, { force: true })
+    service.syncForCurrentSelection()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system-new"}\n', 'utf-8')
+    new CodexRuntimeHomeService(store as never)
+
+    expect(readFileSync(runtimeAuthPath, 'utf-8')).toBe('{"account":"system-new"}\n')
+    expect(
+      existsSync(
+        join(testState.userDataDir, 'codex-runtime-home', 'system-default-runtime-logout.json')
+      )
+    ).toBe(false)
+  })
+
+  it('clears the mirrored runtime auth after an external system-default logout', async () => {
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system"}\n', 'utf-8')
+    const store = createStore(createSettings())
+
+    const { CodexRuntimeHomeService } = await import('./runtime-home-service')
+    const service = new CodexRuntimeHomeService(store as never)
+
+    rmSync(getSystemCodexAuthPath(), { force: true })
+    service.syncForCurrentSelection()
+
+    expect(existsSync(runtimeAuthPath)).toBe(false)
+  })
+
+  it('clears mirrored runtime auth after restart when the system-default auth was deleted', async () => {
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system"}\n', 'utf-8')
+    const settings = createSettings()
+    const store = createStore(settings)
+
+    const { CodexRuntimeHomeService } = await import('./runtime-home-service')
+    new CodexRuntimeHomeService(store as never)
+
+    rmSync(getSystemCodexAuthPath(), { force: true })
+    const restartedService = new CodexRuntimeHomeService(store as never)
+    restartedService.syncForCurrentSelection()
+
+    expect(existsSync(runtimeAuthPath)).toBe(false)
+  })
+
+  it('persists runtime auth refreshes after returning to system default', async () => {
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system"}\n', 'utf-8')
     const managedHomePath = createManagedAuth(
       testState.userDataDir,
       'account-1',
@@ -507,14 +664,16 @@ describe('CodexRuntimeHomeService', () => {
     service.syncForCurrentSelection()
     expect(readFileSync(runtimeAuthPath, 'utf-8')).toBe('{"account":"system"}\n')
 
-    // External tool changes auth — subsequent syncs must not overwrite
+    // Codex used to refresh tokens directly in ~/.codex. With an Orca-owned
+    // runtime home, the same refresh must be read back to the system default.
     writeFileSync(runtimeAuthPath, '{"account":"external-tool"}\n', 'utf-8')
     service.syncForCurrentSelection()
     expect(readFileSync(runtimeAuthPath, 'utf-8')).toBe('{"account":"external-tool"}\n')
+    expect(readFileSync(getSystemCodexAuthPath(), 'utf-8')).toBe('{"account":"external-tool"}\n')
   })
 
   it('removes untrusted runtime auth on restart when persisted active account is invalid', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const settings = createSettings({
       codexManagedAccounts: [
@@ -544,7 +703,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('imports legacy managed-home history into the shared runtime history', async () => {
-    const runtimeHomePath = join(testState.fakeHomeDir, '.codex')
+    const runtimeHomePath = getRuntimeCodexHomePath()
     const runtimeHistoryPath = join(runtimeHomePath, 'history.jsonl')
     writeFileSync(runtimeHistoryPath, '{"id":"shared-1"}\n', 'utf-8')
     const managedHomePath = createManagedAuth(
@@ -575,7 +734,7 @@ describe('CodexRuntimeHomeService', () => {
       return
     }
 
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const managedHomePath = createManagedAuth(
       testState.userDataDir,
@@ -613,7 +772,7 @@ describe('CodexRuntimeHomeService', () => {
       return
     }
 
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const managedHomePath = createManagedAuth(
       testState.userDataDir,
@@ -684,7 +843,7 @@ describe('CodexRuntimeHomeService', () => {
     const { CodexRuntimeHomeService } = await import('./runtime-home-service')
     new CodexRuntimeHomeService(store as never)
 
-    const runtimeHistoryPath = join(testState.fakeHomeDir, '.codex', 'history.jsonl')
+    const runtimeHistoryPath = join(getRuntimeCodexHomePath(), 'history.jsonl')
     expect(readFileSync(runtimeHistoryPath, 'utf-8')).toContain('legacy-1')
 
     writeFileSync(
@@ -701,7 +860,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('clears system-default snapshot via clearSystemDefaultSnapshot', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const store = createStore(createSettings())
 
@@ -720,7 +879,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('reads back CLI-refreshed tokens into managed storage on subsequent sync', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const originalAuth = createCodexAuthJson('user@example.com', 'acct-1', 'original')
     const refreshedAuth = createCodexAuthJson('user@example.com', 'acct-1', 'refreshed')
@@ -747,7 +906,7 @@ describe('CodexRuntimeHomeService', () => {
     const { CodexRuntimeHomeService } = await import('./runtime-home-service')
     const service = new CodexRuntimeHomeService(store as never)
 
-    // Simulate CLI refreshing the token in ~/.codex/auth.json
+    // Simulate CLI refreshing the token in runtime CODEX_HOME/auth.json.
     writeFileSync(runtimeAuthPath, refreshedAuth, 'utf-8')
 
     // Next sync should read back the refreshed token to managed storage
@@ -758,7 +917,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('rejects runtime read-back from a different Codex identity', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const selectedAuth = createCodexAuthJson('selected@example.com', 'acct-selected', 'selected')
     const staleLivePtyAuth = createCodexAuthJson('stale@example.com', 'acct-stale', 'stale')
@@ -795,7 +954,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('routes runtime read-back from a different Codex identity to its matching account', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const account1Auth = createCodexAuthJson('one@example.com', 'acct-one', 'one')
     const account1RefreshedAuth = createCodexAuthJson(
@@ -842,7 +1001,7 @@ describe('CodexRuntimeHomeService', () => {
 
     // An older account-1 Codex process refreshed the shared runtime file after
     // Orca selected account-2. Persist the refresh to account-1, then restore
-    // the selected account in ~/.codex.
+    // the selected account in runtime CODEX_HOME.
     writeFileSync(runtimeAuthPath, account1RefreshedAuth, 'utf-8')
     service.syncForCurrentSelection()
 
@@ -852,7 +1011,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('rejects ambiguous Codex read-back instead of choosing a managed account', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const originalAuth = createCodexAuthJson('same@example.com', 'acct-same', 'original')
     const refreshedAuth = createCodexAuthJson('same@example.com', 'acct-same', 'refreshed')
@@ -914,7 +1073,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('rejects runtime read-back without a positive selected-account identity match', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const selectedAuth = createCodexAuthJson('selected@example.com', 'acct-selected', 'selected')
     const accountOnlyAuth = `${JSON.stringify({
@@ -954,7 +1113,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('rejects same-email runtime read-back when account ids differ from sparse managed metadata', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const selectedAuth = createCodexAuthJson('user@example.com', 'acct-selected', 'selected')
     const staleLivePtyAuth = createCodexAuthJson('user@example.com', 'acct-stale', 'stale')
@@ -989,7 +1148,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('reads back same-account refreshes for sparse managed metadata using stored auth identity', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const originalAuth = createCodexAuthJson('user@example.com', 'acct-selected', 'original')
     const refreshedAuth = createCodexAuthJson('user@example.com', 'acct-selected', 'refreshed')
@@ -1024,7 +1183,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('reads back strong account-id refreshes when the runtime auth has no email', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const originalAuth = createCodexAuthJson('user@example.com', 'acct-1', 'original')
     const refreshedAuth = `${JSON.stringify({
@@ -1064,7 +1223,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('rejects unverifiable Codex read-back on first sync after restart', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"tokens":"refreshed-while-down"}\n', 'utf-8')
     const managedHomePath = createManagedAuth(
       testState.userDataDir,
@@ -1099,7 +1258,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('reads back verified same-account refreshes on first sync after restart', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     const originalAuth = createCodexAuthJson('user@example.com', 'acct-1', 'original', 1_000)
     const refreshedAuth = createCodexAuthJson('user@example.com', 'acct-1', 'refreshed', 2_000)
     writeFileSync(runtimeAuthPath, refreshedAuth, 'utf-8')
@@ -1132,7 +1291,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('rejects older same-account Codex auth on first sync after restart', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     const staleRuntimeAuth = createCodexAuthJson('user@example.com', 'acct-1', 'stale', 1_000)
     const managedAuth = createCodexAuthJson('user@example.com', 'acct-1', 'managed-newer', 2_000)
     writeFileSync(runtimeAuthPath, staleRuntimeAuth, 'utf-8')
@@ -1165,7 +1324,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('does not contaminate the incoming Codex account during account switch', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const managedHomePath1 = createManagedAuth(
       testState.userDataDir,
@@ -1218,7 +1377,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('does not carry the reauth read-back skip across Codex account switches', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const account1Auth = createCodexAuthJson('one@example.com', 'acct-one', 'one')
     const account2Auth = createCodexAuthJson('two@example.com', 'acct-two', 'two')
@@ -1274,7 +1433,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('does not apply inactive-account Codex reauth skip to the active account', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const account1Auth = createCodexAuthJson('one@example.com', 'acct-one', 'one')
     const account1RefreshedAuth = createCodexAuthJson(
@@ -1327,8 +1486,8 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('restores system default when unverified runtime auth appears before deselect', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
-    writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system"}\n', 'utf-8')
     const managedHomePath = createManagedAuth(
       testState.userDataDir,
       'account-1',
@@ -1372,8 +1531,8 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('restores system default after same-identity managed Codex refresh on deselect', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
-    writeFileSync(runtimeAuthPath, '{"account":"system-old"}\n', 'utf-8')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system-old"}\n', 'utf-8')
     const managedAuth = createCodexAuthJson('user@example.com', 'acct-1', 'managed')
     const externalAuth = createCodexAuthJson('user@example.com', 'acct-1', 'external')
     const managedHomePath = createManagedAuth(testState.userDataDir, 'account-1', managedAuth)
@@ -1410,8 +1569,8 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('restores system default when stale Codex credentials are rejected on deselect', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
-    writeFileSync(runtimeAuthPath, '{"account":"system-old"}\n', 'utf-8')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system-old"}\n', 'utf-8')
     const selectedAuth = createCodexAuthJson('selected@example.com', 'acct-selected', 'selected')
     const staleLivePtyAuth = createCodexAuthJson('stale@example.com', 'acct-stale', 'stale')
     const managedHomePath = createManagedAuth(testState.userDataDir, 'account-1', selectedAuth)
@@ -1448,7 +1607,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('keeps external Codex logout when deselecting managed account', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system-old"}\n', 'utf-8')
     const managedHomePath = createManagedAuth(
       testState.userDataDir,
@@ -1484,8 +1643,8 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('captures a fresh system-default snapshot when re-entering managed mode', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
-    writeFileSync(runtimeAuthPath, '{"account":"system-1"}\n', 'utf-8')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system-1"}\n', 'utf-8')
     const managedHomePath = createManagedAuth(
       testState.userDataDir,
       'account-1',
@@ -1514,7 +1673,7 @@ describe('CodexRuntimeHomeService', () => {
 
     settings.activeCodexManagedAccountId = null
     service.syncForCurrentSelection()
-    writeFileSync(runtimeAuthPath, '{"account":"system-2"}\n', 'utf-8')
+    writeFileSync(getSystemCodexAuthPath(), '{"account":"system-2"}\n', 'utf-8')
 
     settings.activeCodexManagedAccountId = 'account-1'
     service.syncForCurrentSelection()
@@ -1525,7 +1684,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('reads back refreshed tokens for the outgoing Codex account before switching', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const account1Original = createCodexAuthJson('one@example.com', 'acct-1', 'one-original')
     const account1Refreshed = createCodexAuthJson('one@example.com', 'acct-1', 'one-refreshed')
@@ -1574,7 +1733,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('does not clobber fresh tokens after clearLastWrittenAuthJson', async () => {
-    const runtimeAuthPath = join(testState.fakeHomeDir, '.codex', 'auth.json')
+    const runtimeAuthPath = getRuntimeCodexAuthPath()
     writeFileSync(runtimeAuthPath, '{"account":"system"}\n', 'utf-8')
     const originalAuth = createCodexAuthJson('user@example.com', 'acct-1', 'original')
     const reauthedAuth = createCodexAuthJson('user@example.com', 'acct-1', 'reauthed')
@@ -1614,7 +1773,7 @@ describe('CodexRuntimeHomeService', () => {
   })
 
   it('preserves conflicting legacy session files under deterministic names', async () => {
-    const runtimeSessionsDir = join(testState.fakeHomeDir, '.codex', 'sessions')
+    const runtimeSessionsDir = join(getRuntimeCodexHomePath(), 'sessions')
     mkdirSync(runtimeSessionsDir, { recursive: true })
     writeFileSync(join(runtimeSessionsDir, 'session.json'), '{"turns":[1]}', 'utf-8')
     const managedHomePath = createManagedAuth(
diff --git a/src/main/codex-accounts/runtime-home-service.ts b/src/main/codex-accounts/runtime-home-service.ts
index 3c099ce575b..3ec807f4143 100644
--- a/src/main/codex-accounts/runtime-home-service.ts
+++ b/src/main/codex-accounts/runtime-home-service.ts
@@ -12,12 +12,12 @@ import {
   rmSync,
   statSync
 } from 'node:fs'
-import { homedir } from 'node:os'
 import { dirname, extname, join, parse, relative } from 'node:path'
 import { app } from 'electron'
 import type { CodexManagedAccount } from '../../shared/types'
 import type { Store } from '../persistence'
 import { writeFileAtomically } from './fs-utils'
+import { getOrcaManagedCodexHomePath, getSystemCodexHomePath } from '../codex/codex-home-paths'
 
 type CodexAuthIdentity = {
   email: string | null
@@ -29,6 +29,11 @@ type CodexSystemDefaultSnapshot = {
   authJson: string | null
 }
 
+type CodexRuntimeLogoutMarker = {
+  systemDefaultAuthJson: string | null
+  loggedOutAt: number
+}
+
 type CodexReadBackResult = 'unchanged' | 'persisted' | 'rejected'
 type CodexReadBackMatch =
   | {
@@ -40,12 +45,11 @@ type CodexReadBackMatch =
   | { kind: 'none' | 'ambiguous' }
 
 export class CodexRuntimeHomeService {
-  // Why: tracks whether auth.json is currently managed by Orca. When null,
-  // Orca does NOT own auth.json and must not overwrite external changes
-  // (e.g. user running `codex login` or another auth tool). The snapshot
-  // restore only fires on the managed→system-default transition.
+  // Why: tracks whether the runtime auth.json currently mirrors a managed
+  // account. When null, runtime auth follows the user's system-default
+  // ~/.codex/auth.json instead of being written back to a managed account.
   private lastSyncedAccountId: string | null = null
-  // Why: tracks the auth.json content Orca last wrote to ~/.codex/auth.json.
+  // Why: tracks the auth.json content Orca last wrote to the runtime CODEX_HOME.
   // Between syncs, if the file differs, Codex CLI refreshed the token — so
   // Orca writes back the refreshed token to managed storage before overwriting.
   // On managed→system-default transition, if the file differs, an external
@@ -77,6 +81,7 @@ export class CodexRuntimeHomeService {
 
   syncForCurrentSelection(): void {
     const settings = this.store.getSettings()
+    const runtimeAuthExistedBeforeSync = existsSync(this.getRuntimeAuthPath())
     if (this.lastSyncedAccountId === null) {
       this.captureSystemDefaultSnapshot({ force: false })
     }
@@ -98,16 +103,30 @@ export class CodexRuntimeHomeService {
       if (settings.activeCodexManagedAccountId) {
         this.store.updateSettings({ activeCodexManagedAccountId: null })
       }
-      // Why: only restore the snapshot when transitioning FROM a managed
-      // account back to system default. When no managed account was ever
-      // active, auth.json belongs to the user and Orca must not touch it.
-      // This prevents overwriting external auth changes (codex login or other
-      // tools) on every PTY launch / rate-limit fetch.
+      // Why: only restore the system-default mirror when transitioning FROM a
+      // managed account. When no managed account was ever active, later syncs
+      // should mirror the user's current ~/.codex/auth.json instead of
+      // replaying an old snapshot on every PTY launch / rate-limit fetch.
       if (this.lastSyncedAccountId !== null) {
         this.restoreSystemDefaultSnapshot({
           detectExternalLogin: outgoingReadBackResult !== 'rejected'
         })
         this.lastSyncedAccountId = null
+      } else if (!runtimeAuthExistedBeforeSync) {
+        if (this.runtimeLogoutMarkerStillApplies()) {
+          this.lastWrittenAuthJson = null
+        } else if (this.lastWrittenAuthJson === null) {
+          // Why: Orca-launched Codex sessions now use an Orca-owned CODEX_HOME
+          // even when no managed account is selected. Seed that runtime home
+          // from the user's current system-default auth once so dev/prod Orca
+          // terminals stay logged in without mutating ~/.codex on startup.
+          this.restoreSystemDefaultSnapshot({ detectExternalLogin: false })
+        } else {
+          this.persistRuntimeLogoutMarker()
+        }
+      } else {
+        this.clearRuntimeLogoutMarker()
+        this.syncRuntimeAuthWithSystemDefault()
       }
       return
     }
@@ -129,10 +148,10 @@ export class CodexRuntimeHomeService {
       this.captureSystemDefaultSnapshot({ force: true })
     }
 
-    // Why: Codex CLI refreshes expired OAuth tokens and writes them back to
-    // ~/.codex/auth.json. If we detect the runtime file differs from what Orca
-    // last wrote, the CLI must have refreshed — so we preserve those tokens
-    // back to managed storage before overwriting runtime with managed state.
+    // Why: Codex CLI refreshes expired OAuth tokens in CODEX_HOME/auth.json.
+    // If we detect the runtime file differs from what Orca last wrote, the CLI
+    // must have refreshed — so we preserve those tokens back to managed
+    // storage before overwriting runtime with managed state.
     if (this.lastSyncedAccountId === activeAccount.id) {
       if (this.skipNextReadBackForAccountId === activeAccount.id) {
         this.skipNextReadBackForAccountId = null
@@ -441,9 +460,7 @@ export class CodexRuntimeHomeService {
   }
 
   private getRuntimeHomePath(): string {
-    const runtimeHomePath = join(homedir(), '.codex')
-    mkdirSync(runtimeHomePath, { recursive: true })
-    return runtimeHomePath
+    return getOrcaManagedCodexHomePath()
   }
 
   private getRuntimeAuthPath(): string {
@@ -454,6 +471,10 @@ export class CodexRuntimeHomeService {
     return join(this.getRuntimeMetadataDir(), 'system-default-auth.json')
   }
 
+  private getRuntimeLogoutMarkerPath(): string {
+    return join(this.getRuntimeMetadataDir(), 'system-default-runtime-logout.json')
+  }
+
   private getRuntimeMetadataDir(): string {
     const metadataDir = join(app.getPath('userData'), 'codex-runtime-home')
     mkdirSync(metadataDir, { recursive: true })
@@ -490,8 +511,8 @@ export class CodexRuntimeHomeService {
     }
 
     // Why: migration is intentionally one-shot. Re-importing every startup
-    // would keep replaying stale managed-home state back into ~/.codex and
-    // make the shared runtime feel nondeterministic.
+    // would keep replaying stale managed-home state back into the shared
+    // runtime and make it feel nondeterministic.
     writeFileAtomically(
       this.getMigrationMarkerPath(),
       `${JSON.stringify({ completedAt: Date.now(), migratedHomeCount: managedHomes.length })}\n`
@@ -618,79 +639,128 @@ export class CodexRuntimeHomeService {
       return
     }
 
-    const runtimeAuthPath = this.getRuntimeAuthPath()
+    const runtimeAuthPath = join(getSystemCodexHomePath(), 'auth.json')
     const snapshot: CodexSystemDefaultSnapshot = {
       authJson: existsSync(runtimeAuthPath) ? readFileSync(runtimeAuthPath, 'utf-8') : null
     }
     writeFileAtomically(snapshotPath, `${JSON.stringify(snapshot, null, 2)}\n`, { mode: 0o600 })
   }
 
-  private restoreSystemDefaultSnapshot(options: { detectExternalLogin: boolean }): void {
-    // Why: detect whether an external tool (e.g. `codex auth login`) overwrote
-    // auth.json while a managed account was active. If so, that external login
-    // becomes the new system default — skip the stale snapshot restore.
-    if (options.detectExternalLogin && this.detectExternalLoginAndUpdateSnapshot()) {
+  private syncRuntimeAuthWithSystemDefault(): void {
+    const runtimeAuthPath = this.getRuntimeAuthPath()
+    const systemDefaultAuthPath = join(getSystemCodexHomePath(), 'auth.json')
+    if (!existsSync(runtimeAuthPath)) {
       return
     }
 
+    try {
+      const runtimeAuth = readFileSync(runtimeAuthPath, 'utf-8')
+      if (!existsSync(systemDefaultAuthPath)) {
+        const snapshot = this.readSystemDefaultSnapshot(this.getSystemDefaultSnapshotPath())
+        const mirroredSystemDefaultAuth =
+          this.lastWrittenAuthJson ?? (snapshot?.authJson !== null ? snapshot?.authJson : null)
+        if (mirroredSystemDefaultAuth !== null && runtimeAuth === mirroredSystemDefaultAuth) {
+          // Why: when the mirrored ~/.codex auth disappears, Orca should treat
+          // that as an external logout for unmanaged sessions instead of
+          // leaving the stale mirrored runtime auth behind after restart.
+          rmSync(runtimeAuthPath, { force: true })
+          this.captureSystemDefaultSnapshot({ force: true })
+          this.lastWrittenAuthJson = null
+        }
+        return
+      }
+      const systemDefaultAuth = readFileSync(systemDefaultAuthPath, 'utf-8')
+      if (runtimeAuth !== systemDefaultAuth) {
+        const snapshot = this.readSystemDefaultSnapshot(this.getSystemDefaultSnapshotPath())
+        const mirroredSystemDefaultAuth =
+          this.lastWrittenAuthJson ?? (snapshot?.authJson !== null ? snapshot?.authJson : null)
+        if (mirroredSystemDefaultAuth !== null && systemDefaultAuth === mirroredSystemDefaultAuth) {
+          // Why: system-default Codex now refreshes tokens inside Orca's
+          // runtime CODEX_HOME. Read that refresh back to ~/.codex so the next
+          // sync does not overwrite fresh runtime credentials with stale ones.
+          this.writeSystemDefaultAuth(runtimeAuth)
+          this.captureSystemDefaultSnapshot({ force: true })
+          this.lastWrittenAuthJson = runtimeAuth
+          return
+        }
+        // Why: the unmanaged path used to read ~/.codex directly. Mirror later
+        // external logins/logouts into Orca's runtime home so ordinary Orca
+        // Codex sessions keep matching the user's current system-default state.
+        this.captureSystemDefaultSnapshot({ force: true })
+        this.writeRuntimeAuth(systemDefaultAuth)
+      }
+    } catch (error) {
+      console.warn('[codex-runtime-home] Failed to sync system-default auth:', error)
+    }
+  }
+
+  private restoreSystemDefaultSnapshot(options: { detectExternalLogin: boolean }): void {
     const snapshotPath = this.getSystemDefaultSnapshotPath()
-    if (!existsSync(snapshotPath)) {
-      rmSync(this.getRuntimeAuthPath(), { force: true })
+    const runtimeAuthPath = this.getRuntimeAuthPath()
+    const systemDefaultAuthPath = join(getSystemCodexHomePath(), 'auth.json')
+    if (options.detectExternalLogin && !existsSync(runtimeAuthPath)) {
+      // Why: once Orca owns the runtime CODEX_HOME, deleting auth.json there is
+      // a local logout signal for Orca-launched Codex sessions, not a reason to
+      // rewrite the user's real ~/.codex snapshot back into place.
+      this.persistRuntimeLogoutMarker()
       this.lastWrittenAuthJson = null
       return
     }
 
+    if (existsSync(systemDefaultAuthPath)) {
+      const systemDefaultAuth = readFileSync(systemDefaultAuthPath, 'utf-8')
+      this.captureSystemDefaultSnapshot({ force: true })
+      this.writeRuntimeAuth(systemDefaultAuth)
+      return
+    }
+
+    if (!existsSync(snapshotPath)) {
+      this.captureSystemDefaultSnapshot({ force: true })
+    }
+
     const snapshot = this.readSystemDefaultSnapshot(snapshotPath)
     if (!snapshot) {
       console.warn('[codex-runtime-home] Ignoring invalid system-default auth snapshot')
       rmSync(snapshotPath, { force: true })
-      rmSync(this.getRuntimeAuthPath(), { force: true })
-      this.lastWrittenAuthJson = null
+      this.captureSystemDefaultSnapshot({ force: true })
+      const refreshedSnapshot = this.readSystemDefaultSnapshot(snapshotPath)
+      if (!refreshedSnapshot) {
+        rmSync(runtimeAuthPath, { force: true })
+        this.lastWrittenAuthJson = null
+        return
+      }
+      if (refreshedSnapshot.authJson === null) {
+        rmSync(runtimeAuthPath, { force: true })
+        this.lastWrittenAuthJson = null
+        return
+      }
+      this.writeRuntimeAuth(refreshedSnapshot.authJson)
       return
     }
     if (snapshot.authJson === null) {
-      rmSync(this.getRuntimeAuthPath(), { force: true })
+      rmSync(runtimeAuthPath, { force: true })
       this.lastWrittenAuthJson = null
       return
     }
     this.writeRuntimeAuth(snapshot.authJson)
   }
 
-  // Why: mirrors ClaudeRuntimeAuthService.detectExternalLoginAndUpdateSnapshot().
-  // If the runtime auth.json differs from what Orca last wrote, something
-  // external changed it. That external state should become the new system
-  // default rather than being overwritten by a potentially stale snapshot.
-  private detectExternalLoginAndUpdateSnapshot(): boolean {
-    if (this.lastWrittenAuthJson === null) {
-      return false
-    }
+  private writeSystemDefaultAuth(contents: string): void {
+    const systemDefaultAuthPath = join(getSystemCodexHomePath(), 'auth.json')
+    mkdirSync(dirname(systemDefaultAuthPath), { recursive: true })
+    writeFileAtomically(systemDefaultAuthPath, contents, { mode: 0o600 })
+    this.ensureOwnerOnlyMode(systemDefaultAuthPath)
+  }
 
-    const runtimeAuthPath = this.getRuntimeAuthPath()
-    if (!existsSync(runtimeAuthPath)) {
-      const snapshotPath = this.getSystemDefaultSnapshotPath()
-      rmSync(snapshotPath, { force: true })
-      this.lastWrittenAuthJson = null
-      return true
-    }
-
-    try {
-      const currentAuth = readFileSync(runtimeAuthPath, 'utf-8')
-      if (currentAuth === this.lastWrittenAuthJson) {
-        return false
-      }
-    } catch {
-      return false
-    }
-
-    const snapshotPath = this.getSystemDefaultSnapshotPath()
-    rmSync(snapshotPath, { force: true })
-    this.lastWrittenAuthJson = null
-    return true
+  private readSystemDefaultAuth(): string | null {
+    const systemDefaultAuthPath = join(getSystemCodexHomePath(), 'auth.json')
+    return existsSync(systemDefaultAuthPath) ? readFileSync(systemDefaultAuthPath, 'utf-8') : null
   }
 
   private writeRuntimeAuth(contents: string): void {
     // Why: auth.json contains sensitive credentials. Restrict to owner-only
     // so other users on a shared Linux/macOS machine cannot read it.
+    this.clearRuntimeLogoutMarker()
     if (this.fileContentsEqual(this.getRuntimeAuthPath(), contents)) {
       this.ensureOwnerOnlyMode(this.getRuntimeAuthPath())
       this.lastWrittenAuthJson = contents
@@ -719,6 +789,58 @@ export class CodexRuntimeHomeService {
     }
   }
 
+  private runtimeLogoutMarkerStillApplies(): boolean {
+    const marker = this.readRuntimeLogoutMarker()
+    if (!marker) {
+      return false
+    }
+    if (this.readSystemDefaultAuth() === marker.systemDefaultAuthJson) {
+      return true
+    }
+    this.clearRuntimeLogoutMarker()
+    return false
+  }
+
+  private persistRuntimeLogoutMarker(systemDefaultAuthJson = this.readSystemDefaultAuth()): void {
+    const marker: CodexRuntimeLogoutMarker = {
+      systemDefaultAuthJson,
+      loggedOutAt: Date.now()
+    }
+    writeFileAtomically(this.getRuntimeLogoutMarkerPath(), `${JSON.stringify(marker, null, 2)}\n`, {
+      mode: 0o600
+    })
+  }
+
+  private readRuntimeLogoutMarker(): CodexRuntimeLogoutMarker | null {
+    let parsed: unknown
+    try {
+      parsed = JSON.parse(readFileSync(this.getRuntimeLogoutMarkerPath(), 'utf-8')) as unknown
+    } catch {
+      return null
+    }
+    if (
+      !parsed ||
+      typeof parsed !== 'object' ||
+      Array.isArray(parsed) ||
+      !('systemDefaultAuthJson' in parsed) ||
+      !('loggedOutAt' in parsed)
+    ) {
+      return null
+    }
+    const marker = parsed as { systemDefaultAuthJson: unknown; loggedOutAt: unknown }
+    if (
+      (marker.systemDefaultAuthJson !== null && typeof marker.systemDefaultAuthJson !== 'string') ||
+      typeof marker.loggedOutAt !== 'number'
+    ) {
+      return null
+    }
+    return marker as CodexRuntimeLogoutMarker
+  }
+
+  private clearRuntimeLogoutMarker(): void {
+    rmSync(this.getRuntimeLogoutMarkerPath(), { force: true })
+  }
+
   private readSystemDefaultSnapshot(snapshotPath: string): CodexSystemDefaultSnapshot | null {
     let rawContents: string
     try {
diff --git a/src/main/codex-usage/scanner.test.ts b/src/main/codex-usage/scanner.test.ts
index d7251b684ea..5d85a30a67e 100644
--- a/src/main/codex-usage/scanner.test.ts
+++ b/src/main/codex-usage/scanner.test.ts
@@ -1,5 +1,56 @@
-import { describe, expect, it } from 'vitest'
-import { attributeCodexUsageEvent, parseCodexUsageRecord } from './scanner'
+import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest'
+import { join } from 'path'
+
+const { getPathMock } = vi.hoisted(() => ({
+  getPathMock: vi.fn<(name: string) => string>()
+}))
+
+vi.mock('electron', () => ({
+  app: {
+    getPath: getPathMock
+  }
+}))
+
+import {
+  attributeCodexUsageEvent,
+  getCodexSessionsDirectory,
+  parseCodexUsageRecord
+} from './scanner'
+
+const originalCodexHome = process.env.CODEX_HOME
+
+beforeEach(() => {
+  delete process.env.CODEX_HOME
+  getPathMock.mockImplementation((name: string) => {
+    if (name === 'userData') {
+      return '/tmp/orca-user-data'
+    }
+    throw new Error(`unexpected app.getPath(${name})`)
+  })
+})
+
+afterEach(() => {
+  if (originalCodexHome === undefined) {
+    delete process.env.CODEX_HOME
+  } else {
+    process.env.CODEX_HOME = originalCodexHome
+  }
+  vi.clearAllMocks()
+})
+
+describe('getCodexSessionsDirectory', () => {
+  it('defaults to Orca-managed Codex runtime sessions', () => {
+    expect(getCodexSessionsDirectory()).toBe(
+      join('/tmp/orca-user-data', 'codex-runtime-home', 'home', 'sessions')
+    )
+  })
+
+  it('respects an explicit CODEX_HOME override', () => {
+    process.env.CODEX_HOME = '/tmp/explicit-codex-home'
+
+    expect(getCodexSessionsDirectory()).toBe(join('/tmp/explicit-codex-home', 'sessions'))
+  })
+})
 
 describe('parseCodexUsageRecord', () => {
   it('uses token totals only as a duplicate baseline', () => {
diff --git a/src/main/codex-usage/scanner.ts b/src/main/codex-usage/scanner.ts
index 130336204db..ef787a8ca4a 100644
--- a/src/main/codex-usage/scanner.ts
+++ b/src/main/codex-usage/scanner.ts
@@ -1,11 +1,11 @@
 /* eslint-disable max-lines -- Why: Codex discovery, incremental parsing, attribution, and aggregation all depend on the same event-normalization rules. Keeping them together makes the duplicate-snapshot logic easier to audit when usage totals look wrong. */
-import { homedir } from 'os'
 import { basename, join, win32, posix } from 'path'
 import { createReadStream } from 'fs'
 import { realpath, readdir, stat } from 'fs/promises'
 import { createInterface } from 'readline'
 import type { Repo } from '../../shared/types'
 import { areWorktreePathsEqual } from '../ipc/worktree-logic'
+import { getOrcaManagedCodexHomePath } from '../codex/codex-home-paths'
 import type {
   CodexUsageAttributedEvent,
   CodexUsageDailyAggregate,
@@ -51,7 +51,6 @@ type CodexUsageDeltaResolution =
   | { kind: 'event'; delta: CodexUsageRawUsage; nextTotals: CodexUsageRawUsage | null }
   | { kind: 'baseline'; nextTotals: CodexUsageRawUsage }
 
-const DEFAULT_CODEX_SESSIONS_DIR = join(homedir(), '.codex', 'sessions')
 const YIELD_EVERY_FILES = 10
 
 function ensureNumber(value: unknown): number {
@@ -112,7 +111,10 @@ export function getCodexSessionsDirectory(): string {
   if (codexHome) {
     return join(codexHome, 'sessions')
   }
-  return DEFAULT_CODEX_SESSIONS_DIR
+  // Why: Orca-launched Codex processes receive an Orca-owned CODEX_HOME, so
+  // the main-process usage scanner must follow that runtime home instead of
+  // the user's ambient ~/.codex directory.
+  return join(getOrcaManagedCodexHomePath(), 'sessions')
 }
 
 export async function listCodexSessionFiles(): Promise<string[]> {
diff --git a/src/main/codex/codex-home-paths.ts b/src/main/codex/codex-home-paths.ts
new file mode 100644
index 00000000000..b3cc67e0b97
--- /dev/null
+++ b/src/main/codex/codex-home-paths.ts
@@ -0,0 +1,14 @@
+import { mkdirSync } from 'node:fs'
+import { homedir } from 'node:os'
+import { join } from 'node:path'
+import { app } from 'electron'
+
+export function getSystemCodexHomePath(): string {
+  return join(homedir(), '.codex')
+}
+
+export function getOrcaManagedCodexHomePath(): string {
+  const managedHomePath = join(app.getPath('userData'), 'codex-runtime-home', 'home')
+  mkdirSync(managedHomePath, { recursive: true })
+  return managedHomePath
+}
diff --git a/src/main/codex/hook-service.test.ts b/src/main/codex/hook-service.test.ts
index a431c17fff9..be76887a3a8 100644
--- a/src/main/codex/hook-service.test.ts
+++ b/src/main/codex/hook-service.test.ts
@@ -1,5 +1,5 @@
 import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest'
-import { mkdtempSync, readFileSync, rmSync } from 'fs'
+import { existsSync, mkdirSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from 'fs'
 import { tmpdir } from 'os'
 import type * as Os from 'os'
 import { join } from 'path'
@@ -48,13 +48,20 @@ afterEach(() => {
 
 describe('CodexHookService', () => {
   it('installs PermissionRequest with trust so Codex approval prompts reach Orca', () => {
+    const systemCodexHome = join(tmpHome, '.codex')
+    mkdirSync(systemCodexHome, { recursive: true })
+    writeFileSync(
+      join(systemCodexHome, 'config.toml'),
+      'model = "gpt-5.2-codex"\napproval_policy = "on-request"\n',
+      'utf-8'
+    )
+
     const status = new CodexHookService().install()
 
     expect(status.state).toBe('installed')
 
-    const hooksConfig = JSON.parse(
-      readFileSync(join(tmpHome, '.codex', 'hooks.json'), 'utf-8')
-    ) as {
+    const managedCodexHome = join(userDataDir, 'codex-runtime-home', 'home')
+    const hooksConfig = JSON.parse(readFileSync(join(managedCodexHome, 'hooks.json'), 'utf-8')) as {
       hooks: Record<string, { hooks?: { command?: string }[] }[]>
     }
 
@@ -71,7 +78,77 @@ describe('CodexHookService', () => {
     expect(hooksConfig.hooks.PermissionRequest?.[0]?.hooks?.[0]?.command).toContain('agent-hooks')
     expect(hooksConfig.hooks.PermissionRequest?.[0]?.hooks?.[0]?.command).toContain('codex-hook')
 
-    const trustConfig = readFileSync(join(tmpHome, '.codex', 'config.toml'), 'utf-8')
+    const trustConfig = readFileSync(join(managedCodexHome, 'config.toml'), 'utf-8')
+    expect(trustConfig).toContain('model = "gpt-5.2-codex"')
+    expect(trustConfig).toContain('approval_policy = "on-request"')
     expect(trustConfig).toContain(':permission_request:0:0')
   })
+
+  it('keeps hooks isolated by Orca userData instead of mutating system ~/.codex', () => {
+    const systemCodexHome = join(tmpHome, '.codex')
+    const systemHooksPath = join(systemCodexHome, 'hooks.json')
+    const existingSystemHooks = '{"hooks":{"Stop":[{"hooks":[{"command":"user-hook"}]}]}}\n'
+    mkdirSync(systemCodexHome, { recursive: true })
+    writeFileSync(systemHooksPath, existingSystemHooks, 'utf-8')
+
+    const devUserDataDir = mkdtempSync(join(tmpdir(), 'orca-dev-codex-user-data-'))
+    const prodUserDataDir = mkdtempSync(join(tmpdir(), 'orca-prod-codex-user-data-'))
+    try {
+      getPathMock.mockImplementation((name: string) => {
+        if (name === 'userData') {
+          return devUserDataDir
+        }
+        throw new Error(`unexpected app.getPath(${name})`)
+      })
+      expect(new CodexHookService().install().state).toBe('installed')
+
+      getPathMock.mockImplementation((name: string) => {
+        if (name === 'userData') {
+          return prodUserDataDir
+        }
+        throw new Error(`unexpected app.getPath(${name})`)
+      })
+      expect(new CodexHookService().install().state).toBe('installed')
+
+      const devHooksPath = join(devUserDataDir, 'codex-runtime-home', 'home', 'hooks.json')
+      const prodHooksPath = join(prodUserDataDir, 'codex-runtime-home', 'home', 'hooks.json')
+      expect(existsSync(devHooksPath)).toBe(true)
+      expect(existsSync(prodHooksPath)).toBe(true)
+      expect(readFileSync(devHooksPath, 'utf-8')).toContain('codex-hook')
+      expect(readFileSync(prodHooksPath, 'utf-8')).toContain('codex-hook')
+      expect(readFileSync(systemHooksPath, 'utf-8')).toBe(existingSystemHooks)
+    } finally {
+      rmSync(devUserDataDir, { recursive: true, force: true })
+      rmSync(prodUserDataDir, { recursive: true, force: true })
+    }
+  })
+
+  it('does not overwrite runtime-only Codex config on hook install', () => {
+    const systemCodexHome = join(tmpHome, '.codex')
+    mkdirSync(systemCodexHome, { recursive: true })
+    writeFileSync(join(systemCodexHome, 'config.toml'), 'model = "system-model"\n', 'utf-8')
+
+    const managedCodexHome = join(userDataDir, 'codex-runtime-home', 'home')
+    mkdirSync(managedCodexHome, { recursive: true })
+    writeFileSync(
+      join(managedCodexHome, 'config.toml'),
+      [
+        'model = "runtime-model"',
+        '',
+        '[projects."/workspace/runtime-only"]',
+        'trust_level = "trusted"',
+        ''
+      ].join('\n'),
+      'utf-8'
+    )
+
+    const status = new CodexHookService().install()
+
+    expect(status.state).toBe('installed')
+    const trustConfig = readFileSync(join(managedCodexHome, 'config.toml'), 'utf-8')
+    expect(trustConfig).toContain('model = "runtime-model"')
+    expect(trustConfig).toContain('[projects."/workspace/runtime-only"]')
+    expect(trustConfig).toContain(':permission_request:0:0')
+    expect(trustConfig).not.toContain('model = "system-model"')
+  })
 })
diff --git a/src/main/codex/hook-service.ts b/src/main/codex/hook-service.ts
index c431b121ce2..6bf511f1b83 100644
--- a/src/main/codex/hook-service.ts
+++ b/src/main/codex/hook-service.ts
@@ -1,5 +1,5 @@
 /* eslint-disable max-lines -- Why: getStatus + install + remove all share the managed-command and trust-key derivation. Splitting would hide that the three operations must agree on group index, event label, and command bytes. */
-import { homedir } from 'os'
+import { existsSync, readFileSync } from 'fs'
 import { join } from 'path'
 import type { SFTPWrapper } from 'ssh2'
 import type { AgentHookInstallState, AgentHookInstallStatus } from '../../shared/agent-hook-types'
@@ -33,6 +33,8 @@ import {
   type CodexHookTrustState,
   type CodexTrustEntry
 } from './config-toml-trust'
+import { writeFileAtomically } from '../codex-accounts/fs-utils'
+import { getOrcaManagedCodexHomePath, getSystemCodexHomePath } from './codex-home-paths'
 
 // Why: PreToolUse/PostToolUse give the dashboard a live readout of the
 // in-flight tool (name + input preview) between UserPromptSubmit and Stop.
@@ -49,11 +51,23 @@ const CODEX_EVENTS = [
 ] as const
 
 function getConfigPath(): string {
-  return join(homedir(), '.codex', 'hooks.json')
+  return join(getOrcaManagedCodexHomePath(), 'hooks.json')
 }
 
 function getCodexConfigTomlPath(): string {
-  return join(homedir(), '.codex', 'config.toml')
+  return join(getOrcaManagedCodexHomePath(), 'config.toml')
+}
+
+function syncSystemConfigIntoManagedCodexHome(): void {
+  const systemConfigPath = join(getSystemCodexHomePath(), 'config.toml')
+  const runtimeConfigPath = getCodexConfigTomlPath()
+  if (!existsSync(systemConfigPath) || existsSync(runtimeConfigPath)) {
+    return
+  }
+  // Why: Orca-launched Codex now reads the Orca-owned runtime CODEX_HOME.
+  // Seed once from the user's real Codex config before appending Orca hook
+  // trust, but never overwrite runtime-only edits Codex made later.
+  writeFileAtomically(runtimeConfigPath, readFileSync(systemConfigPath, 'utf-8'))
 }
 
 // Why: Codex's hash key uses the snake_case event label (see
@@ -326,6 +340,7 @@ export class CodexHookService {
     // pointing at a hook that doesn't exist. Surface failures — without this,
     // getStatus would report green for a hook Codex won't actually fire.
     try {
+      syncSystemConfigIntoManagedCodexHome()
       upsertHookTrustEntries(getCodexConfigTomlPath(), trustEntries)
     } catch (error) {
       return {
@@ -477,9 +492,8 @@ export class CodexHookService {
       const managedEventLabels = new Set<CodexEventLabel>(
         CODEX_EVENTS.map((event) => CODEX_EVENT_LABEL[event])
       )
-      // Why: only drop entries WE wrote. configPath (~/.codex/hooks.json) is
-      // shared with Codex CLI, so user-approved trust entries for non-Orca
-      // commands live in the same `[hooks.state.*]` namespace. Match by hash
+      // Why: only drop entries WE wrote. The same config.toml can contain
+      // user-approved trust entries for non-Orca commands, so match by hash
       // equivalence to our managed command — a sourcePath-only filter would
       // wipe the user's manually-approved entries.
       const ourKeys: string[] = []
diff --git a/src/main/index.ts b/src/main/index.ts
index 149008ea1e1..97b131af52c 100644
--- a/src/main/index.ts
+++ b/src/main/index.ts
@@ -38,7 +38,8 @@ import {
   installDevParentDisconnectQuit,
   installDevParentWatchdog,
   installUncaughtPipeErrorGuard,
-  patchPackagedProcessPath
+  patchPackagedProcessPath,
+  shouldInstallManagedHooks
 } from './startup/configure-process'
 import { startFirstWindowStartupServices } from './startup/first-window-startup-services'
 import { getDevInstanceIdentity } from './startup/dev-instance-identity'
@@ -315,10 +316,7 @@ function openMainWindow(): BrowserWindow {
     window.webContents.id,
     automations,
     {
-      prepareForCodexLaunch: () =>
-        store!.getSettings().activeCodexManagedAccountId
-          ? codexRuntimeHome!.prepareForCodexLaunch()
-          : null,
+      prepareForCodexLaunch: () => codexRuntimeHome!.prepareForCodexLaunch(),
       prepareForClaudeLaunch: () => claudeRuntimeAuth!.prepareForClaudeLaunch()
     },
     agentAwakeService ?? undefined,
@@ -330,10 +328,7 @@ function openMainWindow(): BrowserWindow {
     window,
     store,
     runtime,
-    () =>
-      store!.getSettings().activeCodexManagedAccountId
-        ? codexRuntimeHome!.prepareForCodexLaunch()
-        : null,
+    () => codexRuntimeHome!.prepareForCodexLaunch(),
     () => claudeRuntimeAuth!.prepareForClaudeLaunch()
   )
   rateLimits.attach(window)
@@ -792,10 +787,10 @@ app.whenReady().then(async () => {
   runtimeService.setAutomationService(automations)
   runtimeService.setAccountServices({ claudeAccounts, codexAccounts, rateLimits })
   runtimeService.setCommitMessageAgentEnvironmentResolvers({
-    prepareForCodexLaunch: () =>
-      store!.getSettings().activeCodexManagedAccountId
-        ? codexRuntimeHome!.prepareForCodexLaunch()
-        : null,
+    // Why: local Codex hooks and auth now live in Orca's managed runtime home
+    // even for the system-default path, so every Orca-launched Codex process
+    // must resolve CODEX_HOME through the runtime-home service.
+    prepareForCodexLaunch: () => codexRuntimeHome!.prepareForCodexLaunch(),
     prepareForClaudeLaunch: () => claudeRuntimeAuth!.prepareForClaudeLaunch()
   })
   disposeFeatureWallFirstAgentTour = registerFeatureWallFirstAgentTour({
@@ -811,8 +806,8 @@ app.whenReady().then(async () => {
     })
   )
   nativeTheme.themeSource = store.getSettings().theme ?? 'system'
-  // Why: managed hook installation mutates user-global agent config. Each
-  // installer runs inside its own try/catch so a malformed local config
+  // Why: most managed hook installers still mutate user-global agent config.
+  // Each installer runs inside its own try/catch so a malformed local config
   // (e.g. corrupted ~/.claude/settings.json) cannot brick Orca startup.
   // The agent label travels with each installer so the catch can attribute
   // the failure in the `agent_hook_install_failed` telemetry event.
@@ -826,7 +821,9 @@ app.whenReady().then(async () => {
     ['copilot', () => copilotHookService.install()],
     ['hermes', () => hermesHookService.install()]
   ] as const
-  runManagedHookInstallers(managedHookInstallers)
+  if (shouldInstallManagedHooks(is.dev)) {
+    runManagedHookInstallers(managedHookInstallers)
+  }
 
   app.on('child-process-gone', (_event, details) => {
     recordProcessGoneCrash('child', details.type, details.reason, details.exitCode ?? null, {
diff --git a/src/main/ipc/filesystem.test.ts b/src/main/ipc/filesystem.test.ts
index 6679e5cff26..4f747e36f64 100644
--- a/src/main/ipc/filesystem.test.ts
+++ b/src/main/ipc/filesystem.test.ts
@@ -895,9 +895,7 @@ describe('registerFilesystemHandlers', () => {
     )
   })
 
-  it('preserves the inherited Codex environment when no managed account is selected', async () => {
-    const previousCodexHome = process.env.CODEX_HOME
-    process.env.CODEX_HOME = '/system/codex-home'
+  it('prepares the Orca-managed Codex home for the default system selection', async () => {
     const context = {
       branch: 'feature/ai',
       stagedSummary: 'M\tREADME.md',
@@ -911,26 +909,23 @@ describe('registerFilesystemHandlers', () => {
       message: 'Update README'
     })
 
-    try {
-      registerFilesystemHandlers(store as never, {
-        prepareForCodexLaunch: () => null
-      })
+    registerFilesystemHandlers(store as never, {
+      prepareForCodexLaunch: () => '/orca-managed/codex-home'
+    })
 
-      await handlers.get('git:generateCommitMessage')!(null, {
-        worktreePath: WORKTREE_FEATURE_PATH
-      })
+    await handlers.get('git:generateCommitMessage')!(null, {
+      worktreePath: WORKTREE_FEATURE_PATH
+    })
 
-      expect(generateCommitMessageFromContextMock).toHaveBeenCalledWith(context, params, {
+    expect(generateCommitMessageFromContextMock).toHaveBeenCalledWith(
+      context,
+      params,
+      expect.objectContaining({
         kind: 'local',
-        cwd: WORKTREE_FEATURE_PATH
+        cwd: WORKTREE_FEATURE_PATH,
+        env: expect.objectContaining({ CODEX_HOME: '/orca-managed/codex-home' })
       })
-    } finally {
-      if (previousCodexHome === undefined) {
-        delete process.env.CODEX_HOME
-      } else {
-        process.env.CODEX_HOME = previousCodexHome
-      }
-    }
+    )
   })
 
   it('returns a sanitized error when local agent account preparation fails', async () => {
diff --git a/src/main/ipc/pty.test.ts b/src/main/ipc/pty.test.ts
index 38f15fe68e8..9017b6f2705 100644
--- a/src/main/ipc/pty.test.ts
+++ b/src/main/ipc/pty.test.ts
@@ -666,13 +666,13 @@ describe('registerPtyHandlers', () => {
       expect(env.PATH).toContain('/tmp/orca-user-data/orca-terminal-attribution/posix')
     })
 
-    it('leaves ambient CODEX_HOME untouched when system default is selected', async () => {
+    it('overrides ambient CODEX_HOME with the Orca-managed home for system default', async () => {
       const env = await spawnAndGetEnv(
         undefined,
         { CODEX_HOME: '/tmp/system-codex-home' },
-        () => null
+        () => '/tmp/orca-codex-home'
       )
-      expect(env.CODEX_HOME).toBe('/tmp/system-codex-home')
+      expect(env.CODEX_HOME).toBe('/tmp/orca-codex-home')
     })
 
     describe('daemon-active provider (parity with LocalPtyProvider)', () => {
diff --git a/src/main/ipc/pty.ts b/src/main/ipc/pty.ts
index 4a1454292d6..392964c3ffb 100644
--- a/src/main/ipc/pty.ts
+++ b/src/main/ipc/pty.ts
@@ -338,11 +338,10 @@ export function buildPtyHostEnv(
     }
   }
 
-  // Why: Codex account switching now materializes auth into one shared
-  // runtime home (~/.codex), and Codex launched inside Orca terminals must
-  // use that same prepared home as quota fetches and other entry points.
-  // Keep the override PTY-scoped so Orca does not mutate the app process
-  // environment or the user's unrelated external shells.
+  // Why: Codex account switching now materializes auth into an Orca-scoped
+  // runtime home, and Codex launched inside Orca terminals must use that same
+  // prepared home as quota fetches and other entry points. Keep the override
+  // PTY-scoped so dev/prod Orcas do not share hooks through ~/.codex.
   if (opts.selectedCodexHomePath) {
     baseEnv.CODEX_HOME = opts.selectedCodexHomePath
   }
diff --git a/src/main/startup/configure-process.test.ts b/src/main/startup/configure-process.test.ts
index 2552323e9eb..9ecd76cbddc 100644
--- a/src/main/startup/configure-process.test.ts
+++ b/src/main/startup/configure-process.test.ts
@@ -151,6 +151,20 @@ describe('configureDevUserDataPath', () => {
   })
 })
 
+describe('shouldInstallManagedHooks', () => {
+  it('keeps managed hook auto-install enabled for default dev runs', async () => {
+    const { shouldInstallManagedHooks } = await import('./configure-process')
+
+    expect(shouldInstallManagedHooks(true)).toBe(true)
+  })
+
+  it('allows managed hook auto-install for packaged runs', async () => {
+    const { shouldInstallManagedHooks } = await import('./configure-process')
+
+    expect(shouldInstallManagedHooks(false)).toBe(true)
+  })
+})
+
 describe('installDevParentDisconnectQuit', () => {
   it('quits the dev app when the supervising IPC channel disconnects', async () => {
     const { app } = await import('electron')
diff --git a/src/main/startup/configure-process.ts b/src/main/startup/configure-process.ts
index 7a23599b3b6..6361d502fb3 100644
--- a/src/main/startup/configure-process.ts
+++ b/src/main/startup/configure-process.ts
@@ -126,6 +126,17 @@ export function configureDevUserDataPath(isDev: boolean): void {
   app.setPath('userData', join(app.getPath('appData'), 'orca-dev'))
 }
 
+export function shouldInstallManagedHooks(isDev: boolean): boolean {
+  void isDev
+  // Why: managed hook installation now targets Orca-owned, environment-scoped
+  // homes for Codex rather than the user's default ~/.codex state, so plain
+  // dev runs need the install path enabled to keep hook-backed agent statuses
+  // accurate without an opt-in flag. The remaining agents still rely on the
+  // shared startup installer loop, so keep the policy uniformly on until
+  // they are migrated to more granular ownership seams.
+  return true
+}
+
 export function installDevParentDisconnectQuit(isDev: boolean): void {
   if (!isDev || typeof process.send !== 'function') {
     return