diff --git a/src/renderer/src/components/run-actions/RunActionButton.tsx b/src/renderer/src/components/run-actions/RunActionButton.tsx
index e803e5c5e41..9183a7c3afe 100644
--- a/src/renderer/src/components/run-actions/RunActionButton.tsx
+++ b/src/renderer/src/components/run-actions/RunActionButton.tsx
@@ -10,6 +10,7 @@ import {
   type WorktreeRunActions
 } from '@/lib/run-actions/run-action-config'
 import { startRunAction, stopRunAction } from '@/lib/run-actions/run-action-controller'
+import { autoRunProvisionedWorkspaceOnce } from '@/lib/run-actions/run-action-events'
 import { useWorktreeRunActionRuns, type RunActionRun } from '@/lib/run-actions/run-actions-store'
 import type { WorkspacePort } from '../../../../shared/workspace-ports'
 import { RunActionButtonView } from './RunActionButtonView'
@@ -79,6 +80,11 @@ export function RunActionButton({ worktreeId }: { worktreeId: string }): React.J
     // eslint-disable-next-line react-hooks/exhaustive-deps
     [config, worktreeId, runs]
   )
+  useEffect(() => {
+    if (config?.setupProvisioned) {
+      void autoRunProvisionedWorkspaceOnce(worktreeId, config)
+    }
+  }, [config, worktreeId])
   if (!config || !primary) {
     return null
   }
diff --git a/src/renderer/src/components/terminal-pane/parking/output-watchers/parked-terminal-command-status.ts b/src/renderer/src/components/terminal-pane/parking/output-watchers/parked-terminal-command-status.ts
index 06d1e7b42dd..6e526a0edc0 100644
--- a/src/renderer/src/components/terminal-pane/parking/output-watchers/parked-terminal-command-status.ts
+++ b/src/renderer/src/components/terminal-pane/parking/output-watchers/parked-terminal-command-status.ts
@@ -1,4 +1,5 @@
 /** Keep store-level command status while parked; foreground confirmation and input-intent inference remain with mounted panes. */
+import { parsePaneKey } from '../../../../../../shared/workspace-layout/stable-pane-id'
 import type { AgentStatusEntry } from '../../../../../../shared/agent-status/contracts/agent-status-types'
 import { resolvePaneAgentOwner } from '../../../../../../shared/agent-status/identity/pane-agent-owner'
 import { parseAppSshPtyId } from '../../../../../../shared/ssh-pty-id'
@@ -173,7 +174,12 @@ export function createParkedTerminalCommandStatusPolicy(options: {
         return
       }
       // Commands can change HEAD/index; nudge git UI immediately rather than wait for polling.
-      dispatchTerminalCommandFinishedEvent(worktreeId, bestEffortExitCode, tabId)
+      dispatchTerminalCommandFinishedEvent(
+        worktreeId,
+        bestEffortExitCode,
+        tabId,
+        parsePaneKey(paneKey)?.leafId
+      )
       void retireForegroundAgentUnlessConfirmed()
       // Mirror SSH’s unprobed same-turn drop; local PTYs require mounted foreground confirmation against nested-shell 133;D.
       if (parseAppSshPtyId(ptyId) === null) {
diff --git a/src/renderer/src/components/terminal-pane/pty-connection/agent-identity/pane-agent-identity.ts b/src/renderer/src/components/terminal-pane/pty-connection/agent-identity/pane-agent-identity.ts
index b718f5f481f..8844dc92092 100644
--- a/src/renderer/src/components/terminal-pane/pty-connection/agent-identity/pane-agent-identity.ts
+++ b/src/renderer/src/components/terminal-pane/pty-connection/agent-identity/pane-agent-identity.ts
@@ -1,3 +1,4 @@
+import { parsePaneKey } from '../../../../../../shared/workspace-layout/stable-pane-id'
 import { agentTypeToIconAgent } from '../../../../../../shared/agent-status/presentation/agent-type-icon-agent'
 import { dismissRetainedProgramResult } from '@/lib/program-status/result-retention'
 import { isRetainedProgramResult } from '@/lib/program-status/row'
@@ -217,7 +218,8 @@ export function installPaneAgentIdentity(session: ConnectPanePtySession): void {
     dispatchTerminalCommandFinishedEvent(
       session.deps.worktreeId,
       bestEffortExitCode,
-      session.deps.tabId
+      session.deps.tabId,
+      parsePaneKey(session.cacheKey)?.leafId
     )
     const state = useAppStore.getState()
     const entry = state.agentStatusByPaneKey[session.cacheKey]
diff --git a/src/renderer/src/hooks/terminal-command-finished-event.ts b/src/renderer/src/hooks/terminal-command-finished-event.ts
index 28abe1726df..5b965ee4d80 100644
--- a/src/renderer/src/hooks/terminal-command-finished-event.ts
+++ b/src/renderer/src/hooks/terminal-command-finished-event.ts
@@ -6,13 +6,16 @@ export type TerminalCommandFinishedEventDetail = {
   exitCode: number | null
   /** The pane's tab, when the emitter knows it; consumers tracking one tab's command need it. */
   tabId?: string
+  /** The pane's stable leaf: a split's commands are not the tab's first pane's. */
+  leafId?: string
 }
 
 // Window events let decoupled consumers observe per-pane OSC completion without accessing terminal internals.
 export function dispatchTerminalCommandFinishedEvent(
   worktreeId: string,
   exitCode: number | null,
-  tabId?: string
+  tabId?: string,
+  leafId?: string
 ): void {
   // Why: unit tests and non-DOM renderer shims may expose only the preload API.
   if (typeof window.dispatchEvent !== 'function') {
@@ -21,7 +24,7 @@ export function dispatchTerminalCommandFinishedEvent(
 
   window.dispatchEvent(
     new CustomEvent<TerminalCommandFinishedEventDetail>(ORCA_TERMINAL_COMMAND_FINISHED_EVENT, {
-      detail: { worktreeId, exitCode, ...(tabId ? { tabId } : {}) }
+      detail: { worktreeId, exitCode, ...(tabId ? { tabId } : {}), ...(leafId ? { leafId } : {}) }
     })
   )
 }
diff --git a/src/renderer/src/lib/run-actions/run-action-config.ts b/src/renderer/src/lib/run-actions/run-action-config.ts
index be7d6b2ad80..0ac4ee3ef3f 100644
--- a/src/renderer/src/lib/run-actions/run-action-config.ts
+++ b/src/renderer/src/lib/run-actions/run-action-config.ts
@@ -21,6 +21,8 @@ export type WorktreeRunActions = {
   scripts: OrcaRunScripts
   /** Ids defined by the shared orca.yaml (they need the user's approval before running). */
   sharedIds: ReadonlySet<string>
+  /** The host prepared the checkout itself (setup ran in an environment build, not a Setup tab). */
+  setupProvisioned?: true
 }
 
 export type RunActionTarget = {
@@ -96,13 +98,20 @@ export async function loadWorktreeRunActions(
   }
   const repo = state.repos.find((candidate) => candidate.id === target.repoId)
   let shared: OrcaHooks['scripts'] | undefined
+  let setupProvisioned = false
   try {
     const result = await checkRuntimeHooks(target.hostId, target.repoId, options)
     shared = result.status === 'error' ? undefined : (result.hooks?.scripts ?? undefined)
+    setupProvisioned = result.environmentProvisioned === true
   } catch {
     shared = undefined
   }
-  return mergeRunActions(shared, repo?.hookSettings?.scripts, target.isLocal ? 'local' : 'remote')
+  const merged = mergeRunActions(
+    shared,
+    repo?.hookSettings?.scripts,
+    target.isLocal ? 'local' : 'remote'
+  )
+  return setupProvisioned ? { ...merged, setupProvisioned: true } : merged
 }
 
 /** The action the Run button and shortcut act on: the last one still running here, else the default. */
diff --git a/src/renderer/src/lib/run-actions/run-action-controller.test.ts b/src/renderer/src/lib/run-actions/run-action-controller.test.ts
index 1d1d6d27bba..9f828ebd204 100644
--- a/src/renderer/src/lib/run-actions/run-action-controller.test.ts
+++ b/src/renderer/src/lib/run-actions/run-action-controller.test.ts
@@ -10,6 +10,7 @@ type MockState = {
     { id: string; entityId: string; contentType: string; groupId: string }[]
   >
   ptyIdsByTabId: Record<string, string[]>
+  terminalLayoutsByTabId: Record<string, unknown>
   createTab: ReturnType<typeof vi.fn>
   closeTab: ReturnType<typeof vi.fn>
   setTabCustomTitle: ReturnType<typeof vi.fn>
@@ -69,7 +70,8 @@ vi.stubGlobal('window', new EventTarget())
 const { mergeRunActions, loadWorktreeRunActions } = await import('./run-action-config')
 const { startRunAction, stopRunAction, relaunchInterruptedRunActions, armRunActionRelaunch } =
   await import('./run-action-controller')
-const { installRunActionEvents, armAutoRunAfterSetup } = await import('./run-action-events')
+const { installRunActionEvents, armAutoRunAfterSetup, autoRunProvisionedWorkspaceOnce } =
+  await import('./run-action-events')
 const { getRunActionRun, resetRunActionRunsForTests } = await import('./run-actions-store')
 const { dispatchTerminalCommandFinishedEvent } =
   await import('@/hooks/terminal-command-finished-event')
@@ -90,6 +92,7 @@ function makeState(): MockState {
     tabsByWorktree: {},
     unifiedTabsByWorktree: {},
     ptyIdsByTabId: {},
+    terminalLayoutsByTabId: {},
     createTab: vi.fn((worktreeId: string) => {
       const tab = { id: `tab-${++nextTab}` }
       state.tabsByWorktree[worktreeId] = [...(state.tabsByWorktree[worktreeId] ?? []), tab]
@@ -322,6 +325,73 @@ describe('run actions', () => {
     expect(await startRunAction(WT_B, web, config([web]))).toBe(false)
   })
 
+  it('a command finishing in a split of the run tab does not end the run', async () => {
+    await startRunAction(WT_A, web, config([web]))
+    const { tabId } = getRunActionRun(WT_A, 'web')!
+    const L1 = '11111111-1111-4111-8111-111111111111'
+    const L2 = '22222222-2222-4222-8222-222222222222'
+    const notifyLayouts = (): void => {
+      for (const listener of mocks.subscribers) {
+        listener(state, { tabsByWorktree: state.tabsByWorktree, terminalLayoutsByTabId: {} })
+      }
+    }
+    state.terminalLayoutsByTabId = { [tabId]: { root: { type: 'leaf', leafId: L1 } } }
+    notifyLayouts()
+    expect(getRunActionRun(WT_A, 'web')?.leafId).toBe(L1)
+    state.terminalLayoutsByTabId = {
+      [tabId]: {
+        root: {
+          type: 'split',
+          direction: 'vertical',
+          first: { type: 'leaf', leafId: L1 },
+          second: { type: 'leaf', leafId: L2 }
+        }
+      }
+    }
+    notifyLayouts()
+    dispatchTerminalCommandFinishedEvent(WT_A, 0, tabId, L2)
+    expect(getRunActionRun(WT_A, 'web')?.status).toBe('running')
+    dispatchTerminalCommandFinishedEvent(WT_A, 1, tabId, L1)
+    expect(getRunActionRun(WT_A, 'web')).toMatchObject({ status: 'failed', exitCode: 1 })
+  })
+
+  it('ignores a pane it cannot attribute while the tab has several panes', async () => {
+    await startRunAction(WT_A, web, config([web]))
+    const { tabId } = getRunActionRun(WT_A, 'web')!
+    state.terminalLayoutsByTabId = {
+      [tabId]: {
+        root: {
+          type: 'split',
+          direction: 'vertical',
+          first: { type: 'leaf', leafId: '11111111-1111-4111-8111-111111111111' },
+          second: { type: 'leaf', leafId: '22222222-2222-4222-8222-222222222222' }
+        }
+      }
+    }
+    dispatchTerminalCommandFinishedEvent(WT_A, 0, tabId, '22222222-2222-4222-8222-222222222222')
+    expect(getRunActionRun(WT_A, 'web')?.status).toBe('running')
+  })
+
+  it('auto-runs once on first open when the host ran setup in the environment build', async () => {
+    const storage = new Map<string, string>()
+    vi.stubGlobal('localStorage', {
+      getItem: (key: string) => storage.get(key) ?? null,
+      setItem: (key: string, value: string) => void storage.set(key, value)
+    })
+    try {
+      const provisioned = { ...config([web]), setupProvisioned: true as const }
+      provisioned.scripts = { ...provisioned.scripts, autoRunAfterSetup: true }
+      expect(await autoRunProvisionedWorkspaceOnce(WT_A, provisioned)).toBe(true)
+      expect(getRunActionRun(WT_A, 'web')?.status).toBe('running')
+      dispatchTerminalCommandFinishedEvent(WT_A, 0, getRunActionRun(WT_A, 'web')!.tabId)
+      expect(await autoRunProvisionedWorkspaceOnce(WT_A, provisioned)).toBe(false)
+      const notProvisioned = { ...provisioned, setupProvisioned: undefined }
+      expect(await autoRunProvisionedWorkspaceOnce(WT_B, notProvisioned)).toBe(false)
+    } finally {
+      vi.stubGlobal('localStorage', undefined)
+    }
+  })
+
   it('auto-runs the default action once setup succeeds, not when it fails', async () => {
     mocks.checkRuntimeHooks.mockResolvedValue({
       status: 'ok',
diff --git a/src/renderer/src/lib/run-actions/run-action-controller.ts b/src/renderer/src/lib/run-actions/run-action-controller.ts
index a2dc704c290..d060e038a86 100644
--- a/src/renderer/src/lib/run-actions/run-action-controller.ts
+++ b/src/renderer/src/lib/run-actions/run-action-controller.ts
@@ -21,7 +21,7 @@ import {
   type RunActionTarget,
   type WorktreeRunActions
 } from './run-action-config'
-import { findLiveRunTabId, sameRunTab } from './run-action-tabs'
+import { findLiveRunTabId, runPanePtyId, sameRunTab } from './run-action-tabs'
 
 /** Conductor's grace period: an interrupted dev server gets this long before its shell is closed. */
 export const RUN_ACTION_STOP_GRACE_MS = 5_000
@@ -101,8 +101,7 @@ async function stopRunActionOnce(worktreeId: string, actionId: string): Promise<
     return
   }
   const state = useAppStore.getState()
-  const liveTabId = findLiveRunTabId(state, worktreeId, run.tabId)
-  const ptyId = liveTabId ? state.ptyIdsByTabId[liveTabId]?.[0] : undefined
+  const ptyId = runPanePtyId(state, worktreeId, run.tabId, run.leafId)
   if (!ptyId) {
     deleteRunActionRun(worktreeId, actionId)
     return
diff --git a/src/renderer/src/lib/run-actions/run-action-events.ts b/src/renderer/src/lib/run-actions/run-action-events.ts
index a29bdf4e3bb..609db852b4b 100644
--- a/src/renderer/src/lib/run-actions/run-action-events.ts
+++ b/src/renderer/src/lib/run-actions/run-action-events.ts
@@ -13,10 +13,15 @@ import {
   findRunActionRunByTab,
   getRunActionRun,
   listRunActionRuns,
-  patchRunActionRun
+  patchRunActionRun,
+  type RunActionRun
 } from './run-actions-store'
-import { loadWorktreeRunActions, pickPrimaryRunAction } from './run-action-config'
-import { findLiveRunTabId, sameRunTab } from './run-action-tabs'
+import {
+  loadWorktreeRunActions,
+  pickPrimaryRunAction,
+  type WorktreeRunActions
+} from './run-action-config'
+import { findLiveRunTabId, runPanePtyId, runTabLeafIds, sameRunTab } from './run-action-tabs'
 import {
   isRunActionRelaunchArmed,
   notifyRunActionStopped,
@@ -59,6 +64,10 @@ function handleCommandFinished(detail: TerminalCommandFinishedEventDetail): void
   if (!run || (run.status !== 'running' && run.status !== 'stopping')) {
     return
   }
+  if (!isRunPane(run, detail.leafId)) {
+    // A command finished in a split of the run's tab, not the action itself.
+    return
+  }
   // OSC 133;D may omit the exit code; without one the run is only known to have ended.
   const status =
     run.status === 'stopping'
@@ -70,6 +79,31 @@ function handleCommandFinished(detail: TerminalCommandFinishedEventDetail): void
   notifyRunActionStopped(tabId)
 }
 
+function isRunPane(run: RunActionRun, leafId: string | undefined): boolean {
+  if (!leafId) {
+    return true
+  }
+  if (run.leafId) {
+    return run.leafId === leafId
+  }
+  // The run's pane isn't known yet: only a tab with one pane proves which pane finished.
+  const leaves = runTabLeafIds(useAppStore.getState(), run.worktreeId, run.tabId)
+  return leaves.length <= 1
+}
+
+/** A run learns its pane while its tab still has exactly one, before any split exists. */
+function learnRunPanes(state: AppState): void {
+  for (const run of listRunActionRuns()) {
+    if (run.leafId) {
+      continue
+    }
+    const leaves = runTabLeafIds(state, run.worktreeId, run.tabId)
+    if (leaves.length === 1) {
+      patchRunActionRun(run.worktreeId, run.actionId, { leafId: leaves[0] })
+    }
+  }
+}
+
 function pruneClosedRunTabs(state: AppState): void {
   for (const run of listRunActionRuns()) {
     // A restarting host rebuilds its tab list; the relaunch owns these runs until it settles.
@@ -91,6 +125,42 @@ function pruneClosedRunTabs(state: AppState): void {
   }
 }
 
+const AUTO_RAN_KEY = 'orca.runActions.autoRan.v1'
+
+function readAutoRan(): string[] {
+  try {
+    const parsed: unknown = JSON.parse(globalThis.localStorage?.getItem(AUTO_RAN_KEY) ?? '[]')
+    return Array.isArray(parsed) ? parsed.filter((id): id is string => typeof id === 'string') : []
+  } catch {
+    return []
+  }
+}
+
+/**
+ * The host ran setup while building the environment, so no Setup tab will ever finish here:
+ * honor `autoRunAfterSetup` the first time the workspace is opened, once per workspace.
+ */
+export async function autoRunProvisionedWorkspaceOnce(
+  worktreeId: string,
+  config: WorktreeRunActions
+): Promise<boolean> {
+  const action = config.setupProvisioned ? pickAutoRunAction(config.scripts) : null
+  const autoRan = readAutoRan()
+  if (!action || autoRan.includes(worktreeId) || getRunActionRun(worktreeId, action.id)) {
+    return false
+  }
+  try {
+    // Recorded before starting, so a second open (or window) can't start it twice.
+    globalThis.localStorage?.setItem(
+      AUTO_RAN_KEY,
+      JSON.stringify([...autoRan, worktreeId].slice(-500))
+    )
+  } catch {
+    // Best effort: without storage this still runs once per window session.
+  }
+  return startRunAction(worktreeId, action, config, { activate: false })
+}
+
 /** Follows run terminals: their exits update status, and closing one forgets its run. */
 export function installRunActionEvents(): () => void {
   const onFinished = (event: Event): void => {
@@ -104,6 +174,9 @@ export function installRunActionEvents(): () => void {
   let pruneTimer: ReturnType<typeof setTimeout> | null = null
   const installedAt = Date.now()
   const unsubscribe = useAppStore.subscribe((state, previous) => {
+    if (state.terminalLayoutsByTabId !== previous.terminalLayoutsByTabId) {
+      learnRunPanes(state)
+    }
     if (state.tabsByWorktree === previous.tabsByWorktree || pruneTimer) {
       return
     }
@@ -136,8 +209,7 @@ const STARTUP_PRUNE_GRACE_MS = 15_000
 async function reconcileLocalRunsAfterStartup(): Promise<void> {
   const state = useAppStore.getState()
   for (const run of listRunActionRuns()) {
-    const liveTabId = findLiveRunTabId(state, run.worktreeId, run.tabId)
-    const ptyId = liveTabId ? state.ptyIdsByTabId[liveTabId]?.[0] : undefined
+    const ptyId = runPanePtyId(state, run.worktreeId, run.tabId, run.leafId)
     if (run.status !== 'running' || !ptyId || getRemoteRuntimePtyOwner(ptyId)) {
       continue
     }
diff --git a/src/renderer/src/lib/run-actions/run-action-tabs.ts b/src/renderer/src/lib/run-actions/run-action-tabs.ts
index b1b00ee5471..4310b155267 100644
--- a/src/renderer/src/lib/run-actions/run-action-tabs.ts
+++ b/src/renderer/src/lib/run-actions/run-action-tabs.ts
@@ -1,4 +1,5 @@
 import type { AppState } from '@/store/types'
+import type { TerminalPaneLayoutNode } from '../../../../shared/workspace-layout/terminal-tab-types'
 
 /** A remote host adopts a tab the window created under `web-terminal-<id>`; both name one tab. */
 const MIRRORED_TAB_PREFIX = 'web-terminal-'
@@ -21,3 +22,43 @@ export function findLiveRunTabId(
     (state.tabsByWorktree[worktreeId] ?? []).find((tab) => sameRunTab(tab.id, tabId))?.id ?? null
   )
 }
+
+function collectLeafIds(node: TerminalPaneLayoutNode | null | undefined, out: string[]): string[] {
+  if (!node) {
+    return out
+  }
+  if (node.type === 'leaf') {
+    out.push(node.leafId)
+  } else {
+    collectLeafIds(node.first, out)
+    collectLeafIds(node.second, out)
+  }
+  return out
+}
+
+/** Every pane of the run's tab, in layout order. */
+export function runTabLeafIds(
+  state: Pick<AppState, 'tabsByWorktree' | 'terminalLayoutsByTabId'>,
+  worktreeId: string,
+  tabId: string
+): string[] {
+  const liveTabId = findLiveRunTabId(state, worktreeId, tabId)
+  return liveTabId ? collectLeafIds(state.terminalLayoutsByTabId?.[liveTabId]?.root, []) : []
+}
+
+/** The PTY of the run's own pane, falling back to the tab's first PTY. */
+export function runPanePtyId(
+  state: Pick<AppState, 'tabsByWorktree' | 'terminalLayoutsByTabId' | 'ptyIdsByTabId'>,
+  worktreeId: string,
+  tabId: string,
+  leafId: string | undefined
+): string | undefined {
+  const liveTabId = findLiveRunTabId(state, worktreeId, tabId)
+  if (!liveTabId) {
+    return undefined
+  }
+  const byLeaf = leafId
+    ? state.terminalLayoutsByTabId?.[liveTabId]?.ptyIdsByLeafId?.[leafId]
+    : undefined
+  return byLeaf ?? state.ptyIdsByTabId[liveTabId]?.[0]
+}
diff --git a/src/renderer/src/lib/run-actions/run-actions-store.ts b/src/renderer/src/lib/run-actions/run-actions-store.ts
index 363fb0310d3..803167d10a1 100644
--- a/src/renderer/src/lib/run-actions/run-actions-store.ts
+++ b/src/renderer/src/lib/run-actions/run-actions-store.ts
@@ -11,6 +11,8 @@ export type RunActionRun = {
   actionName: string
   /** The terminal tab showing this run's output. */
   tabId: string
+  /** The tab's pane running the action (learned once the pane exists); splits are other panes. */
+  leafId?: string
   status: RunActionStatus
   exitCode: number | null
   startedAt: number
@@ -40,7 +42,8 @@ function readRun(value: unknown): RunActionRun | null {
     return null
   }
   const run: Record<string, unknown> = { ...value }
-  const { worktreeId, repoId, actionId, actionName, tabId, status, exitCode, startedAt } = run
+  const { worktreeId, repoId, actionId, actionName, tabId, status, exitCode, startedAt, leafId } =
+    run
   if (
     typeof worktreeId !== 'string' ||
     typeof repoId !== 'string' ||
@@ -60,7 +63,8 @@ function readRun(value: unknown): RunActionRun | null {
     tabId,
     status: STATUSES.find((known) => known === status) ?? 'exited',
     exitCode: typeof exitCode === 'number' ? exitCode : null,
-    startedAt
+    startedAt,
+    ...(typeof leafId === 'string' ? { leafId } : {})
   }
 }
 
@@ -124,7 +128,7 @@ export function setRunActionRun(run: RunActionRun): void {
 export function patchRunActionRun(
   worktreeId: string,
   actionId: string,
-  patch: Partial<Pick<RunActionRun, 'status' | 'exitCode'>>
+  patch: Partial<Pick<RunActionRun, 'status' | 'exitCode' | 'leafId'>>
 ): void {
   const current = runs[worktreeId]?.[actionId]
   if (!current) {