diff --git a/desktop/src/pages/ComputerUseSettings.test.tsx b/desktop/src/pages/ComputerUseSettings.test.tsx
index a31b720f..e2b05ade 100644
--- a/desktop/src/pages/ComputerUseSettings.test.tsx
+++ b/desktop/src/pages/ComputerUseSettings.test.tsx
@@ -50,6 +50,14 @@ const enabledConfig = {
   },
 }
 
+function deferred<T>() {
+  let resolve!: (value: T) => void
+  const promise = new Promise<T>(res => {
+    resolve = res
+  })
+  return { promise, resolve }
+}
+
 describe('ComputerUseSettings', () => {
   beforeEach(() => {
     useSettingsStore.setState({ locale: 'en' })
@@ -95,4 +103,114 @@ describe('ComputerUseSettings', () => {
       enabled: false,
     })
   })
+
+  it('keeps the user-selected enablement when a stale refresh resolves later', async () => {
+    const staleRefresh = deferred<typeof enabledConfig>()
+    computerUseApiMock.getStatus.mockResolvedValue({
+      ...readyStatus,
+      venv: {
+        ...readyStatus.venv,
+        created: true,
+      },
+      dependencies: {
+        ...readyStatus.dependencies,
+        installed: true,
+      },
+    })
+    computerUseApiMock.getInstalledApps.mockResolvedValue({ apps: [] })
+    computerUseApiMock.getAuthorizedApps
+      .mockResolvedValueOnce({
+        ...enabledConfig,
+        enabled: false,
+      })
+      .mockReturnValueOnce(staleRefresh.promise)
+
+    render(<ComputerUseSettings />)
+
+    const toggle = await screen.findByLabelText('Enabled')
+    await waitFor(() => expect(toggle).not.toBeChecked())
+    await waitFor(() => expect(computerUseApiMock.getInstalledApps).toHaveBeenCalled())
+
+    await act(async () => {
+      fireEvent.click(toggle)
+      await Promise.resolve()
+    })
+
+    expect(toggle).toBeChecked()
+
+    await act(async () => {
+      staleRefresh.resolve({
+        ...enabledConfig,
+        enabled: false,
+      })
+      await staleRefresh.promise
+    })
+
+    expect(toggle).toBeChecked()
+  })
+
+  it('saves app and grant flag changes from the ready environment view', async () => {
+    computerUseApiMock.getStatus.mockResolvedValue({
+      ...readyStatus,
+      venv: {
+        ...readyStatus.venv,
+        created: true,
+      },
+      dependencies: {
+        ...readyStatus.dependencies,
+        installed: true,
+      },
+    })
+    computerUseApiMock.getInstalledApps.mockResolvedValue({
+      apps: [
+        {
+          bundleId: 'com.example.Preview',
+          displayName: 'Preview',
+          path: '/Applications/Preview.app',
+        },
+      ],
+    })
+
+    render(<ComputerUseSettings />)
+
+    await screen.findByText('Preview')
+
+    await act(async () => {
+      fireEvent.click(screen.getByText('Preview'))
+      await Promise.resolve()
+    })
+
+    expect(computerUseApiMock.setAuthorizedApps).toHaveBeenCalledWith({
+      authorizedApps: [
+        expect.objectContaining({
+          bundleId: 'com.example.Preview',
+          displayName: 'Preview',
+        }),
+      ],
+      grantFlags: {
+        clipboardRead: true,
+        clipboardWrite: true,
+        systemKeyCombos: true,
+      },
+    })
+
+    await act(async () => {
+      fireEvent.click(screen.getByLabelText('Clipboard Access'))
+      await Promise.resolve()
+    })
+
+    expect(computerUseApiMock.setAuthorizedApps).toHaveBeenCalledWith({
+      authorizedApps: [
+        expect.objectContaining({
+          bundleId: 'com.example.Preview',
+          displayName: 'Preview',
+        }),
+      ],
+      grantFlags: {
+        clipboardRead: false,
+        clipboardWrite: false,
+        systemKeyCombos: true,
+      },
+    })
+  })
 })
diff --git a/desktop/src/pages/ComputerUseSettings.tsx b/desktop/src/pages/ComputerUseSettings.tsx
index 4e81efc4..9cfd2556 100644
--- a/desktop/src/pages/ComputerUseSettings.tsx
+++ b/desktop/src/pages/ComputerUseSettings.tsx
@@ -1,4 +1,4 @@
-import { useState, useEffect, useCallback, useMemo } from 'react'
+import { useState, useEffect, useCallback, useMemo, useRef } from 'react'
 import { computerUseApi, type ComputerUseStatus, type SetupResult, type InstalledApp, type AuthorizedApp } from '../api/computerUse'
 import { useTranslation } from '../i18n'
 
@@ -61,6 +61,7 @@ export function ComputerUseSettings() {
   const [computerUseEnabled, setComputerUseEnabled] = useState(true)
   const [clipboardAccess, setClipboardAccess] = useState(true)
   const [systemKeys, setSystemKeys] = useState(true)
+  const configMutationSeqRef = useRef(0)
 
   const fetchStatus = useCallback(async () => {
     setCheckState('loading')
@@ -73,7 +74,11 @@ export function ComputerUseSettings() {
     }
   }, [])
 
-  const applyConfig = useCallback((configResult: Awaited<ReturnType<typeof computerUseApi.getAuthorizedApps>>) => {
+  const applyConfig = useCallback((
+    configResult: Awaited<ReturnType<typeof computerUseApi.getAuthorizedApps>>,
+    requestSeq = configMutationSeqRef.current,
+  ) => {
+    if (requestSeq !== configMutationSeqRef.current) return
     setComputerUseEnabled(configResult.enabled)
     setAuthorizedApps(configResult.authorizedApps)
     setAuthorizedBundleIds(new Set(configResult.authorizedApps.map(a => a.bundleId)))
@@ -82,14 +87,16 @@ export function ComputerUseSettings() {
   }, [])
 
   const fetchConfig = useCallback(async () => {
+    const requestSeq = configMutationSeqRef.current
     try {
-      applyConfig(await computerUseApi.getAuthorizedApps())
+      applyConfig(await computerUseApi.getAuthorizedApps(), requestSeq)
     } catch {
       // API not ready
     }
   }, [applyConfig])
 
   const fetchApps = useCallback(async () => {
+    const requestSeq = configMutationSeqRef.current
     setAppsLoading(true)
     try {
       const [appsResult, configResult] = await Promise.all([
@@ -97,7 +104,7 @@ export function ComputerUseSettings() {
         computerUseApi.getAuthorizedApps(),
       ])
       setInstalledApps(appsResult.apps)
-      applyConfig(configResult)
+      applyConfig(configResult, requestSeq)
     } catch {
       // API not ready
     } finally {
@@ -132,6 +139,7 @@ export function ComputerUseSettings() {
   }
 
   const toggleApp = (app: InstalledApp) => {
+    configMutationSeqRef.current += 1
     const newSet = new Set(authorizedBundleIds)
     let newAuthorized = [...authorizedApps]
     if (newSet.has(app.bundleId)) {
@@ -159,6 +167,7 @@ export function ComputerUseSettings() {
   }
 
   const toggleFlag = (flag: 'clipboard' | 'systemKeys', value: boolean) => {
+    configMutationSeqRef.current += 1
     if (flag === 'clipboard') setClipboardAccess(value)
     else setSystemKeys(value)
 
@@ -173,6 +182,7 @@ export function ComputerUseSettings() {
   }
 
   const toggleComputerUseEnabled = (value: boolean) => {
+    configMutationSeqRef.current += 1
     setComputerUseEnabled(value)
     computerUseApi.setAuthorizedApps({ enabled: value }).then(() => {
       setAppsSaved(true)