diff --git a/desktop/src/components/chat/MessageList.test.tsx b/desktop/src/components/chat/MessageList.test.tsx
index a4020499..e5cb3874 100644
--- a/desktop/src/components/chat/MessageList.test.tsx
+++ b/desktop/src/components/chat/MessageList.test.tsx
@@ -3093,6 +3093,241 @@ describe('MessageList nested tool calls', () => {
     expect(screen.queryByRole('button', { name: 'Latest' })).toBeNull()
   })
 
+  it('keeps a pending file permission pinned when its preview grows after render', async () => {
+    const observers: Array<{
+      callback: ResizeObserverCallback
+      targets: Element[]
+    }> = []
+    class TestResizeObserver {
+      targets: Element[] = []
+      observe = vi.fn((target: Element) => {
+        this.targets.push(target)
+      })
+      unobserve = vi.fn()
+      disconnect = vi.fn()
+
+      constructor(callback: ResizeObserverCallback) {
+        observers.push({ callback, targets: this.targets })
+      }
+    }
+    vi.stubGlobal('ResizeObserver', TestResizeObserver)
+
+    const pendingPermission = {
+      requestId: 'permission-write-memory',
+      toolName: 'Write',
+      input: {
+        file_path: '/tmp/MEMORY.md',
+        content: Array.from({ length: 80 }, (_, index) => `Memory line ${index}`).join('\n'),
+      },
+    }
+    useChatStore.setState({
+      sessions: {
+        [ACTIVE_TAB]: makeSessionState({
+          chatState: 'permission_pending',
+          pendingPermission,
+          pendingPermissions: {
+            [pendingPermission.requestId]: pendingPermission,
+          },
+          messages: [
+            ...Array.from({ length: 130 }, (_, index) => ({
+              id: `assistant-history-${index}`,
+              type: 'assistant_text' as const,
+              content: `History line ${index}`,
+              timestamp: index,
+            })),
+            {
+              id: 'permission-write-memory-message',
+              type: 'permission_request',
+              requestId: pendingPermission.requestId,
+              toolName: pendingPermission.toolName,
+              input: pendingPermission.input,
+              timestamp: 131,
+            },
+          ],
+        }),
+      },
+    })
+
+    const { container } = render(<MessageList />)
+    const scroller = container.querySelector('.chat-scroll-area') as HTMLDivElement
+    const scrollContent = scroller.firstElementChild as HTMLElement
+    let scrollTop = 15000
+    let scrollHeight = 15521
+    Object.defineProperty(scroller, 'scrollHeight', {
+      configurable: true,
+      get: () => scrollHeight,
+    })
+    Object.defineProperty(scroller, 'clientHeight', { configurable: true, value: 521 })
+    Object.defineProperty(scroller, 'scrollTop', {
+      configurable: true,
+      get: () => scrollTop,
+      set: (value) => {
+        scrollTop = value
+      },
+    })
+
+    await waitForProgrammaticScrollReset()
+    fireEvent.scroll(scroller)
+    const allowButton = await screen.findByRole('button', { name: 'Allow: /tmp/MEMORY.md' })
+
+    const contentObserver = observers.find(({ targets }) => targets.includes(scrollContent))
+    expect(contentObserver).toBeTruthy()
+    const permissionItem = allowButton.closest('[data-virtual-message-item]') as HTMLElement
+    expect(permissionItem).toBeTruthy()
+    const permissionItemObserver = observers.find(({ targets }) => targets.includes(permissionItem))
+    expect(permissionItemObserver).toBeTruthy()
+
+    scrollHeight = 15717
+    fireEvent.scroll(scroller)
+    act(() => {
+      permissionItemObserver?.callback([{
+        contentRect: { height: 520 },
+        target: permissionItem,
+      } as unknown as ResizeObserverEntry], {} as ResizeObserver)
+    })
+    act(() => {
+      contentObserver?.callback([{
+        contentRect: { height: 15717 },
+        target: scrollContent,
+      } as unknown as ResizeObserverEntry], {} as ResizeObserver)
+    })
+
+    expect(scrollTop).toBe(15196)
+    expect(screen.queryByRole('button', { name: 'Latest' })).toBeNull()
+  })
+
+  it('does not follow resize for stale permission state without a pending file permission', async () => {
+    let resizeCallback: ResizeObserverCallback | null = null
+    class TestResizeObserver {
+      observe = vi.fn()
+      unobserve = vi.fn()
+      disconnect = vi.fn()
+
+      constructor(callback: ResizeObserverCallback) {
+        resizeCallback = callback
+      }
+    }
+    vi.stubGlobal('ResizeObserver', TestResizeObserver)
+
+    useChatStore.setState({
+      sessions: {
+        [ACTIVE_TAB]: makeSessionState({
+          chatState: 'permission_pending',
+          messages: [{
+            id: 'assistant-restored',
+            type: 'assistant_text',
+            content: 'Restored completed response',
+            timestamp: 1,
+          }],
+        }),
+      },
+    })
+
+    const { container } = render(<MessageList />)
+    const scroller = container.querySelector('.chat-scroll-area') as HTMLDivElement
+    let scrollTop = 600
+    let scrollHeight = 1000
+    Object.defineProperty(scroller, 'scrollHeight', {
+      configurable: true,
+      get: () => scrollHeight,
+    })
+    Object.defineProperty(scroller, 'clientHeight', { configurable: true, value: 400 })
+    Object.defineProperty(scroller, 'scrollTop', {
+      configurable: true,
+      get: () => scrollTop,
+      set: (value) => {
+        scrollTop = value
+      },
+    })
+
+    await waitForProgrammaticScrollReset()
+    fireEvent.scroll(scroller)
+
+    scrollHeight = 1400
+    act(() => {
+      resizeCallback?.([{
+        contentRect: { height: 1400 },
+      } as ResizeObserverEntry], {} as ResizeObserver)
+    })
+
+    expect(scrollTop).toBe(600)
+  })
+
+  it('preserves upward wheel and keyboard intent while a pending file permission preview resizes', async () => {
+    let resizeCallback: ResizeObserverCallback | null = null
+    class TestResizeObserver {
+      observe = vi.fn()
+      unobserve = vi.fn()
+      disconnect = vi.fn()
+
+      constructor(callback: ResizeObserverCallback) {
+        resizeCallback = callback
+      }
+    }
+    vi.stubGlobal('ResizeObserver', TestResizeObserver)
+
+    const pendingPermission = {
+      requestId: 'permission-write-memory-wheel',
+      toolName: 'Write',
+      input: {
+        file_path: '/tmp/MEMORY.md',
+        content: 'Remember this preference',
+      },
+    }
+    useChatStore.setState({
+      sessions: {
+        [ACTIVE_TAB]: makeSessionState({
+          chatState: 'permission_pending',
+          pendingPermission,
+          pendingPermissions: {
+            [pendingPermission.requestId]: pendingPermission,
+          },
+          messages: [{
+            id: 'permission-write-memory-wheel-message',
+            type: 'permission_request',
+            requestId: pendingPermission.requestId,
+            toolName: pendingPermission.toolName,
+            input: pendingPermission.input,
+            timestamp: 1,
+          }],
+        }),
+      },
+    })
+
+    const { container } = render(<MessageList />)
+    const scroller = container.querySelector('.chat-scroll-area') as HTMLDivElement
+    let scrollTop = 600
+    let scrollHeight = 1000
+    Object.defineProperty(scroller, 'scrollHeight', {
+      configurable: true,
+      get: () => scrollHeight,
+    })
+    Object.defineProperty(scroller, 'clientHeight', { configurable: true, value: 400 })
+    Object.defineProperty(scroller, 'scrollTop', {
+      configurable: true,
+      get: () => scrollTop,
+      set: (value) => {
+        scrollTop = value
+      },
+    })
+
+    await waitForProgrammaticScrollReset()
+    fireEvent.scroll(scroller)
+
+    fireEvent.wheel(scroller, { deltaY: -120 })
+    fireEvent.keyDown(scroller, { key: 'PageUp', shiftKey: false })
+    fireEvent.keyDown(scroller, { key: 'ArrowDown', shiftKey: false })
+    scrollTop = 300
+    scrollHeight = 1400
+    act(() => {
+      resizeCallback?.([{
+        contentRect: { height: 1400 },
+      } as ResizeObserverEntry], {} as ResizeObserver)
+    })
+
+    expect(scrollTop).toBe(300)
+  })
+
   it('lets the user drag away from active thinking output before the programmatic scroll settles', async () => {
     let resizeCallback: ResizeObserverCallback | null = null
     class TestResizeObserver {
diff --git a/desktop/src/components/chat/MessageList.tsx b/desktop/src/components/chat/MessageList.tsx
index d49b7900..685d8ace 100644
--- a/desktop/src/components/chat/MessageList.tsx
+++ b/desktop/src/components/chat/MessageList.tsx
@@ -949,6 +949,7 @@ const VIRTUAL_MAX_ITEM_HEIGHT = 24_000
 // Windows WebView2 can report 1px oscillations for live chat content; don't
 // convert those into bottom-scroll corrections.
 const CONTENT_RESIZE_FOLLOW_MIN_DELTA_PX = 2
+const USER_SCROLL_INTENT_WINDOW_MS = 500
 const CONVERSATION_NAVIGATION_MIN_ITEMS = 4
 const STREAMING_ASSISTANT_NAVIGATION_KEY = 'streaming-assistant-message'
 const EMPTY_MESSAGES: UIMessage[] = []
@@ -1432,14 +1433,19 @@ export function MessageList({ sessionId, compact = false }: MessageListProps = {
   const activeThinkingId = sessionState?.activeThinkingId ?? null
   const agentTaskNotifications = sessionState?.agentTaskNotifications ?? EMPTY_AGENT_TASK_NOTIFICATIONS
   const hasRunningBackgroundTasks = hasAnyRunningBackgroundTasks(sessionState?.backgroundAgentTasks)
+  const pendingPermissions = listPendingPermissions(sessionState)
   const activeAskUserQuestionToolUseId =
-    listPendingPermissions(sessionState)
+    pendingPermissions
       .find((permission) => permission.toolName === 'AskUserQuestion')?.toolUseId ?? null
+  const hasPendingPermissionCard = pendingPermissions.some(
+    (permission) => permission.toolName !== 'AskUserQuestion',
+  )
   const shouldFollowContentResize =
     streamingText.trim().length > 0 ||
     chatState === 'streaming' ||
     chatState === 'compacting' ||
     chatState === 'tool_executing' ||
+    hasPendingPermissionCard ||
     (chatState === 'thinking' && Boolean(activeThinkingId))
   const scrollContainerRef = useRef<HTMLDivElement>(null)
   const scrollContentRef = useRef<HTMLDivElement>(null)
@@ -1458,6 +1464,7 @@ export function MessageList({ sessionId, compact = false }: MessageListProps = {
   const isProgrammaticScrollingRef = useRef(false)
   const ignoreProgrammaticScrollUntilRef = useRef(0)
   const ignoreProgrammaticScrollTopRef = useRef<number | null>(null)
+  const userScrollIntentUntilRef = useRef(0)
   const lastSessionIdRef = useRef<string | null | undefined>(resolvedSessionId)
   const lastTailMessageIdBySessionRef = useRef(new Map<string, string | null>())
   const t = useTranslation()
@@ -1570,6 +1577,9 @@ export function MessageList({ sessionId, compact = false }: MessageListProps = {
     if (previousHeight !== undefined && Math.abs(previousHeight - measuredHeight) < 1) return
 
     virtualItemHeightsRef.current.set(itemKey, measuredHeight)
+    if (hasPendingPermissionCard && shouldAutoScrollRef.current) {
+      scrollToBottom('auto')
+    }
 
     if (typeof requestAnimationFrame === 'undefined') {
       pendingMeasuredHeightsRef.current = true
@@ -1584,7 +1594,7 @@ export function MessageList({ sessionId, compact = false }: MessageListProps = {
         flushMeasuredHeightVersion()
       })
     }
-  }, [flushMeasuredHeightVersion])
+  }, [flushMeasuredHeightVersion, hasPendingPermissionCard, scrollToBottom])
 
   const updateAutoScrollState = useCallback(() => {
     // Ignore scroll events triggered by our own programmatic scrolling to
@@ -1606,13 +1616,52 @@ export function MessageList({ sessionId, compact = false }: MessageListProps = {
     }
     syncVirtualViewportFromContainer(container)
     const isAtBottom = isNearScrollBottom(container)
+    const isPermissionLayoutShift =
+      hasPendingPermissionCard &&
+      shouldAutoScrollRef.current &&
+      !isAtBottom &&
+      performance.now() >= userScrollIntentUntilRef.current
+    if (isPermissionLayoutShift) return
+
     shouldAutoScrollRef.current = isAtBottom
     setShowJumpToLatest(!isAtBottom)
 
     if (resolvedSessionId) {
       rememberSessionScroll(resolvedSessionId, container)
     }
-  }, [resolvedSessionId, syncVirtualViewportFromContainer])
+  }, [hasPendingPermissionCard, resolvedSessionId, syncVirtualViewportFromContainer])
+
+  const markUserScrollIntent = useCallback(() => {
+    userScrollIntentUntilRef.current = performance.now() + USER_SCROLL_INTENT_WINDOW_MS
+  }, [])
+
+  const handleWheelScrollIntent = useCallback((event: { deltaY: number }) => {
+    markUserScrollIntent()
+    if (event.deltaY < 0) {
+      shouldAutoScrollRef.current = false
+      setShowJumpToLatest(true)
+    }
+  }, [markUserScrollIntent])
+
+  const handleKeyDownScrollIntent = useCallback((event: { key: string; shiftKey: boolean }) => {
+    const isUpwardScrollKey =
+      event.key === 'ArrowUp' ||
+      event.key === 'PageUp' ||
+      event.key === 'Home' ||
+      (event.key === ' ' && event.shiftKey)
+    const isScrollKey = isUpwardScrollKey ||
+      event.key === 'ArrowDown' ||
+      event.key === 'PageDown' ||
+      event.key === 'End' ||
+      event.key === ' '
+    if (!isScrollKey) return
+
+    markUserScrollIntent()
+    if (isUpwardScrollKey) {
+      shouldAutoScrollRef.current = false
+      setShowJumpToLatest(true)
+    }
+  }, [markUserScrollIntent])
 
   useLayoutEffect(() => {
     if (lastSessionIdRef.current !== resolvedSessionId) {
@@ -2187,6 +2236,10 @@ export function MessageList({ sessionId, compact = false }: MessageListProps = {
       <div
         ref={scrollContainerRef}
         onScroll={updateAutoScrollState}
+        onWheel={handleWheelScrollIntent}
+        onPointerDown={markUserScrollIntent}
+        onTouchStart={markUserScrollIntent}
+        onKeyDown={handleKeyDownScrollIntent}
         className={`${CHAT_SCROLL_AREA_CLASS} h-full overflow-y-auto ${compact ? 'px-3 py-3 pb-5' : 'px-4 py-4'}`}
       >
         <div