diff --git a/notes/project-first-host-model-change-inventory.md b/notes/project-first-host-model-change-inventory.md
index d925e5c4f57..8be4deece45 100644
--- a/notes/project-first-host-model-change-inventory.md
+++ b/notes/project-first-host-model-change-inventory.md
@@ -483,11 +483,14 @@ Already partially landed:
 - inline `Run on` import-existing-folder setup for known hosts where the
   selected project is not set up yet
 - inline `Run on` clone setup for not-yet-set-up non-SSH local/runtime hosts
+- repo-backed setup method metadata so imported/cloned setup methods survive
+  compatibility projection and persistence sync
 
 Not complete yet:
 
 - SSH clone/provision flows
-- durable cloned setup metadata while `Repo` remains the compatibility source
+- independent project-host setup persistence beyond the repo-backed
+  compatibility records
 - bulk setup flows and setup for hosts that are not already known to the client
 - project settings split into global and host-specific ownership
 - host settings/capability UI aligned with project setup
diff --git a/notes/project-first-host-model-handoff.md b/notes/project-first-host-model-handoff.md
index 65ace713f35..8766bdc22fc 100644
--- a/notes/project-first-host-model-handoff.md
+++ b/notes/project-first-host-model-handoff.md
@@ -408,11 +408,13 @@ Already partially landed:
 - inline import-existing-folder setup from the composer
 - inline clone setup from the composer for not-yet-set-up non-SSH
   local/runtime hosts
+- repo-backed setup method metadata for imported/cloned project-host setups
 
 Still needed:
 
 - finish SSH clone/provision flows
-- durable cloned setup metadata while `Repo` remains the compatibility source
+- independent project-host setup persistence beyond the repo-backed
+  compatibility records
 - bulk setup flows and setup for newly added hosts
 - project settings split into global and host-specific ownership
 - host settings/capability UI aligned with project setup
diff --git a/notes/project-first-host-model.md b/notes/project-first-host-model.md
index 12df69c887a..21b8937144c 100644
--- a/notes/project-first-host-model.md
+++ b/notes/project-first-host-model.md
@@ -755,15 +755,18 @@ Landed so far:
   lets the user paste a different URL, clones into the selected parent
   directory through the existing local/runtime clone APIs, then links the
   resulting checkout as the project's host setup.
+- Added repo-backed setup method metadata so imported and cloned setup flows
+  survive persistence/projection sync as `imported-existing-folder` or `cloned`
+  while `Repo` remains the compatibility source of truth.
 - Added tests for local repos, SSH repos, same-provider multi-host grouping,
   no-identity same-name non-grouping, selector cache behavior, persistence
   backfill, repo mutation synchronization, renderer hydration, runtime RPC
-  routing, local/runtime clone setup composition, and GitHub clone URL
-  inference. Sidebar row-builder tests now cover project-first multi-host
-  grouping and same-name repo separation without project identity. Workspace
-  target tests cover local-only fallback, focused-host setup selection, explicit
-  project-plus-host resolution, same-name non-merging, and unavailable setup
-  reasons.
+  routing, setup method persistence, local/runtime clone setup composition, and
+  GitHub clone URL inference. Sidebar row-builder tests now cover project-first
+  multi-host grouping and same-name repo separation without project identity.
+  Workspace target tests cover local-only fallback, focused-host setup
+  selection, explicit project-plus-host resolution, same-name non-merging, and
+  unavailable setup reasons.
 
 Important limitation:
 
@@ -778,9 +781,9 @@ Important limitation:
   folder today; true SSH clone should either reuse a remote git-provider exec
   path or add a remote clone flow with progress, abort, safe path derivation,
   cleanup, and auth parity.
-- The current clone setup action records the resulting checkout by calling the
-  existing-folder setup path, so durable `setupMethod: cloned` semantics are not
-  complete while the compatibility projection remains repo-backed.
+- Project-host setup records are still regenerated from repo compatibility
+  records. The setup method now persists through that projection, but the final
+  independent setup table is still future work.
 
 Remaining end-to-end work:
 
diff --git a/src/main/ipc/repos.ts b/src/main/ipc/repos.ts
index 98f34d59ac8..6214e9cd679 100644
--- a/src/main/ipc/repos.ts
+++ b/src/main/ipc/repos.ts
@@ -99,7 +99,8 @@ function buildProjectHostSetupResult(store: Store, repo: Repo): ProjectHostSetup
 function alignRepoWithRequestedProject(
   store: Store,
   repo: Repo,
-  projectId: string
+  projectId: string,
+  setupMethod: ProjectHostSetupExistingFolderArgs['setupMethod'] = 'imported-existing-folder'
 ): ProjectHostSetupResult {
   let setup = getProjectHostSetupForRepo(store.getProjectHostSetups(), repo)
   if (setup.projectId !== projectId) {
@@ -122,6 +123,13 @@ function alignRepoWithRequestedProject(
     repo = updated
     setup = getProjectHostSetupForRepo(store.getProjectHostSetups(), repo)
   }
+  const updated = store.updateRepo(repo.id, { projectHostSetupMethod: setupMethod })
+  if (!updated) {
+    throw new Error(
+      `Project setup repo disappeared before setup metadata could be linked: ${repo.id}`
+    )
+  }
+  repo = updated
   return buildProjectHostSetupResult(store, repo)
 }
 
@@ -329,7 +337,8 @@ const ProjectHostSetupExistingFolderIpcArgs = z.object({
   hostId: z.string().min(1),
   path: z.string().min(1),
   kind: z.enum(['git', 'folder']).optional(),
-  displayName: z.string().min(1).optional()
+  displayName: z.string().min(1).optional(),
+  setupMethod: z.enum(['imported-existing-folder', 'cloned']).optional()
 })
 
 const ProjectGroupScanNestedArgs = z.object({
@@ -691,7 +700,7 @@ export function registerRepoHandlers(mainWindow: BrowserWindow, store: Store): v
       invalidateAuthorizedRootsCache()
       notifyReposChanged(mainWindow)
       emitRepoAdded('folder_picker', result.alreadyExisted)
-      return alignRepoWithRequestedProject(store, result.repo, args.projectId)
+      return alignRepoWithRequestedProject(store, result.repo, args.projectId, args.setupMethod)
     }
   )
 
diff --git a/src/main/persistence.test.ts b/src/main/persistence.test.ts
index 27c1ab0c78c..a325c3f70ad 100644
--- a/src/main/persistence.test.ts
+++ b/src/main/persistence.test.ts
@@ -2329,6 +2329,21 @@ describe('Store', () => {
     ])
   })
 
+  it('updateRepo preserves repo-backed project host setup method', async () => {
+    const store = await createStore()
+    store.addRepo(makeRepo())
+
+    store.updateRepo('r1', { projectHostSetupMethod: 'cloned' })
+
+    expect(store.getRepo('r1')?.projectHostSetupMethod).toBe('cloned')
+    expect(store.getProjectHostSetups()).toEqual([
+      expect.objectContaining({
+        id: 'r1',
+        setupMethod: 'cloned'
+      })
+    ])
+  })
+
   it('updateRepo drops repo icons that fail shared sanitization', async () => {
     const store = await createStore()
     store.addRepo(makeRepo())
diff --git a/src/main/persistence.ts b/src/main/persistence.ts
index e6d2bf1118f..680e332479a 100644
--- a/src/main/persistence.ts
+++ b/src/main/persistence.ts
@@ -36,6 +36,7 @@ import type {
   PersistedState,
   Project,
   ProjectHostSetup,
+  ProjectHostSetupMethod,
   Repo,
   ProjectGroup,
   SparsePreset,
@@ -741,8 +742,19 @@ function sanitizeRepoUpstream(value: unknown): Repo['upstream'] | undefined {
   return owner && repo ? { owner, repo } : undefined
 }
 
+function sanitizeRepoProjectHostSetupMethod(
+  value: unknown
+): Exclude<ProjectHostSetupMethod, 'legacy-repo'> | undefined {
+  return value === 'imported-existing-folder' || value === 'cloned' ? value : undefined
+}
+
 function sanitizeRepoUpdatesForPersistence<
-  T extends Partial<Pick<Repo, 'badgeColor' | 'repoIcon' | 'upstream' | 'worktreeBasePath'>>
+  T extends Partial<
+    Pick<
+      Repo,
+      'badgeColor' | 'repoIcon' | 'upstream' | 'worktreeBasePath' | 'projectHostSetupMethod'
+    >
+  >
 >(updates: T): T {
   const sanitized = { ...updates }
   if ('badgeColor' in sanitized) {
@@ -777,6 +789,14 @@ function sanitizeRepoUpdatesForPersistence<
       delete sanitized.worktreeBasePath
     }
   }
+  if ('projectHostSetupMethod' in sanitized) {
+    const setupMethod = sanitizeRepoProjectHostSetupMethod(sanitized.projectHostSetupMethod)
+    if (setupMethod === undefined) {
+      delete sanitized.projectHostSetupMethod
+    } else {
+      sanitized.projectHostSetupMethod = setupMethod
+    }
+  }
   return sanitized
 }
 
@@ -2696,6 +2716,7 @@ export class Store {
         | 'externalWorktreeVisibilityPromptDismissedAt'
         | 'projectGroupId'
         | 'projectGroupOrder'
+        | 'projectHostSetupMethod'
       >
     > & { sourceControlAi?: Repo['sourceControlAi'] | null }
   ): Repo | null {
@@ -2780,11 +2801,13 @@ export class Store {
       repoIcon: rawRepoIcon,
       upstream: rawUpstream,
       sourceControlAi: rawSourceControlAi,
+      projectHostSetupMethod: rawProjectHostSetupMethod,
       ...repoWithoutIcon
     } = repo
     const repoIcon = sanitizeRepoIcon(rawRepoIcon)
     const upstream = sanitizeRepoUpstream(rawUpstream)
     const sourceControlAi = normalizeRepoSourceControlAiOverrides(rawSourceControlAi)
+    const projectHostSetupMethod = sanitizeRepoProjectHostSetupMethod(rawProjectHostSetupMethod)
     const gitUsername = isFolderRepo(repo)
       ? ''
       : (this.gitUsernameCache.get(repo.path) ??
@@ -2799,6 +2822,7 @@ export class Store {
       ...(repoIcon !== undefined ? { repoIcon } : {}),
       ...(upstream !== undefined ? { upstream } : {}),
       ...(sourceControlAi !== undefined ? { sourceControlAi } : {}),
+      ...(projectHostSetupMethod !== undefined ? { projectHostSetupMethod } : {}),
       kind: isFolderRepo(repo) ? 'folder' : 'git',
       gitUsername,
       hookSettings: {
diff --git a/src/main/runtime/orca-runtime.ts b/src/main/runtime/orca-runtime.ts
index 8a30bdf496a..2961549073d 100644
--- a/src/main/runtime/orca-runtime.ts
+++ b/src/main/runtime/orca-runtime.ts
@@ -6484,6 +6484,15 @@ export class OrcaRuntimeService {
       repo = updated
       setup = getProjectHostSetupForRepo(this.listProjectHostSetups(), repo)
     }
+    const setupMethod = args.setupMethod ?? 'imported-existing-folder'
+    const updated = this.store.updateRepo(repo.id, { projectHostSetupMethod: setupMethod })
+    if (!updated) {
+      throw new Error(
+        `Project setup repo disappeared before setup metadata could be linked: ${repo.id}`
+      )
+    }
+    repo = updated
+    setup = getProjectHostSetupForRepo(this.listProjectHostSetups(), repo)
     const project = this.listProjects().find((entry) => entry.id === setup.projectId)
     if (!project) {
       throw new Error(`Project setup was created without a project record: ${setup.projectId}`)
diff --git a/src/main/runtime/rpc/methods/project-runtime-rpc-methods.ts b/src/main/runtime/rpc/methods/project-runtime-rpc-methods.ts
index 858f09d6eaf..c8ee8bcfd0f 100644
--- a/src/main/runtime/rpc/methods/project-runtime-rpc-methods.ts
+++ b/src/main/runtime/rpc/methods/project-runtime-rpc-methods.ts
@@ -15,7 +15,8 @@ const ProjectHostSetupExistingFolder = z.object({
   }),
   path: requiredString('Missing project path'),
   kind: z.enum(['git', 'folder']).optional(),
-  displayName: OptionalString
+  displayName: OptionalString,
+  setupMethod: z.enum(['imported-existing-folder', 'cloned']).optional()
 })
 
 export const PROJECT_RUNTIME_METHODS: RpcMethod[] = [
diff --git a/src/main/runtime/rpc/methods/repo.test.ts b/src/main/runtime/rpc/methods/repo.test.ts
index e5d269c2c68..9a11e934a0f 100644
--- a/src/main/runtime/rpc/methods/repo.test.ts
+++ b/src/main/runtime/rpc/methods/repo.test.ts
@@ -388,7 +388,8 @@ describe('repo RPC methods', () => {
         projectId: 'project-1',
         hostId: 'runtime:env-1',
         path: '/repo',
-        kind: 'git'
+        kind: 'git',
+        setupMethod: 'cloned'
       })
     )
 
@@ -396,7 +397,8 @@ describe('repo RPC methods', () => {
       projectId: 'project-1',
       hostId: 'runtime:env-1',
       path: '/repo',
-      kind: 'git'
+      kind: 'git',
+      setupMethod: 'cloned'
     })
     expect(response).toMatchObject({ ok: true, result: { result } })
   })
diff --git a/src/renderer/src/store/slices/repos.test.ts b/src/renderer/src/store/slices/repos.test.ts
index 2394ffc1aeb..0362a4e71cd 100644
--- a/src/renderer/src/store/slices/repos.test.ts
+++ b/src/renderer/src/store/slices/repos.test.ts
@@ -431,7 +431,7 @@ describe('repo slice runtime routing', () => {
       path: clonedRepo.path,
       displayName: clonedRepo.displayName,
       setupState: 'ready',
-      setupMethod: 'legacy-repo',
+      setupMethod: 'cloned',
       createdAt: 1,
       updatedAt: 1
     }
@@ -462,7 +462,8 @@ describe('repo slice runtime routing', () => {
       hostId: 'local',
       path: clonedRepo.path,
       kind: 'git',
-      displayName: 'Project'
+      displayName: 'Project',
+      setupMethod: 'cloned'
     })
   })
 
@@ -484,7 +485,7 @@ describe('repo slice runtime routing', () => {
       path: clonedRepo.path,
       displayName: clonedRepo.displayName,
       setupState: 'ready',
-      setupMethod: 'legacy-repo',
+      setupMethod: 'cloned',
       createdAt: 1,
       updatedAt: 1
     }
@@ -534,7 +535,8 @@ describe('repo slice runtime routing', () => {
         hostId: 'runtime:env-1',
         path: clonedRepo.path,
         kind: 'git',
-        displayName: 'Project'
+        displayName: 'Project',
+        setupMethod: 'cloned'
       },
       timeoutMs: 15_000
     })
diff --git a/src/renderer/src/store/slices/repos.ts b/src/renderer/src/store/slices/repos.ts
index 3454e786583..fbd3b047235 100644
--- a/src/renderer/src/store/slices/repos.ts
+++ b/src/renderer/src/store/slices/repos.ts
@@ -747,7 +747,8 @@ export const createRepoSlice: StateCreator<AppState, [], [], RepoSlice> = (set,
         hostId: args.hostId,
         path: repo.path,
         kind: 'git',
-        displayName: args.displayName
+        displayName: args.displayName,
+        setupMethod: 'cloned'
       })
     } catch (err) {
       console.error('Failed to clone project on host:', err)
diff --git a/src/shared/project-host-setup-projection.test.ts b/src/shared/project-host-setup-projection.test.ts
index b4198265c17..465cac1e8bd 100644
--- a/src/shared/project-host-setup-projection.test.ts
+++ b/src/shared/project-host-setup-projection.test.ts
@@ -71,6 +71,19 @@ describe('project host setup projection', () => {
     })
   })
 
+  it('preserves repo-backed setup method metadata', () => {
+    const projection = projectHostSetupProjectionFromRepos([
+      repo({
+        id: 'repo-1',
+        path: '/Users/alice/orca',
+        displayName: 'orca',
+        projectHostSetupMethod: 'cloned'
+      })
+    ])
+
+    expect(projection.setups[0]?.setupMethod).toBe('cloned')
+  })
+
   it('groups repo checkouts with the same provider identity under one project', () => {
     const projection = projectHostSetupProjectionFromRepos([
       repo({
diff --git a/src/shared/project-host-setup-projection.ts b/src/shared/project-host-setup-projection.ts
index fd553c9d7bf..4e3a1b17705 100644
--- a/src/shared/project-host-setup-projection.ts
+++ b/src/shared/project-host-setup-projection.ts
@@ -68,6 +68,7 @@ function mergeProjectRepo(project: Project, repo: Repo): Project {
 function createSetupFromRepo(repo: Repo, projectId: string, now: number): ProjectHostSetup {
   const hostId = getRepoExecutionHostId(repo)
   const createdAt = repo.addedAt || now
+  const setupMethod = repo.projectHostSetupMethod ?? 'legacy-repo'
   return {
     id: repo.id,
     projectId,
@@ -83,7 +84,7 @@ function createSetupFromRepo(repo: Repo, projectId: string, now: number): Projec
     ...(repo.gitUsername ? { gitUsername: repo.gitUsername } : {}),
     ...(repo.sourceControlAi ? { sourceControlAi: repo.sourceControlAi } : {}),
     setupState: 'ready',
-    setupMethod: 'legacy-repo',
+    setupMethod,
     createdAt,
     updatedAt: createdAt
   }
diff --git a/src/shared/types.ts b/src/shared/types.ts
index 7d0cb1e0c2d..4ecbb573482 100644
--- a/src/shared/types.ts
+++ b/src/shared/types.ts
@@ -131,6 +131,7 @@ export type ProjectHostSetupExistingFolderArgs = {
   path: string
   kind?: RepoKind
   displayName?: string
+  setupMethod?: Exclude<ProjectHostSetupMethod, 'legacy-repo'>
 }
 
 export type ProjectHostSetupCloneArgs = {
@@ -193,6 +194,8 @@ export type Repo = {
   projectGroupOrder?: number
   /** Repo-specific source-control AI overrides. Missing fields inherit global settings. */
   sourceControlAi?: RepoSourceControlAiOverrides
+  /** Transitional source for ProjectHostSetup.setupMethod while Repo remains compatibility storage. */
+  projectHostSetupMethod?: Exclude<ProjectHostSetupMethod, 'legacy-repo'>
 }
 
 export type ProjectGroupCreatedFrom = 'manual' | 'folder-scan' | 'migration'