diff --git a/packages/app/e2e/browser/assistant-file-link-tooltip.spec.ts b/packages/app/e2e/browser/assistant-file-link-tooltip.spec.ts
new file mode 100644
index 0000000000..69cccc52dd
--- /dev/null
+++ b/packages/app/e2e/browser/assistant-file-link-tooltip.spec.ts
@@ -0,0 +1,69 @@
+import { writeFile } from "node:fs/promises";
+import path from "node:path";
+import { test, expect, type Page } from "../support/fixtures";
+import { openAgentRoute, seedMockAgentWorkspace } from "../support/helpers/mock-agent";
+
+async function readFileLinkTooltip(page: Page): Promise<void> {
+  const link = page.getByRole("link", { name: "the guide", exact: true });
+  await link.hover();
+  await expect(page.getByRole("tooltip")).toContainText("guide.md");
+}
+
+async function leaveFileLink(page: Page): Promise<void> {
+  await page.mouse.move(5, 5);
+  await expect(page.getByRole("tooltip")).toHaveCount(0);
+}
+
+async function openLinkedFile(page: Page): Promise<void> {
+  await page.getByRole("link", { name: "the guide", exact: true }).click();
+  await expect(page.getByTestId("markdown-preview-frame")).toContainText("Example guide");
+  await leaveFileLink(page);
+}
+
+async function returnToAgent(page: Page): Promise<void> {
+  await page.getByRole("button", { name: "Tooltip regression", exact: true }).click();
+  await expect(page.getByRole("link", { name: "the guide", exact: true })).toBeVisible();
+  await leaveFileLink(page);
+}
+
+async function switchToFileTab(page: Page): Promise<void> {
+  await page.getByRole("button", { name: "guide.md", exact: true }).click();
+  await expect(page.getByTestId("markdown-preview-frame")).toContainText("Example guide");
+  await leaveFileLink(page);
+}
+
+test("opening an assistant file link dismisses its tooltip over the file tab", async ({
+  page,
+}, testInfo) => {
+  testInfo.setTimeout(120_000);
+  const agent = await seedMockAgentWorkspace({
+    repoPrefix: "tooltip-5811-",
+    title: "Tooltip regression",
+    featureValues: {
+      mockStreamingAssistantResponse: "Read [the guide](./guide.md).",
+      mockStreamingAssistantIntervalMs: 5,
+    },
+  });
+  try {
+    await writeFile(
+      path.join(agent.cwd, "guide.md"),
+      "# Example guide\n\n" + "Plain paragraph.\n\n".repeat(150),
+    );
+    await openAgentRoute(page, agent);
+    await agent.client.sendAgentMessage(agent.agentId, "Show the file link.");
+    await agent.client.waitForFinish(agent.agentId, 30_000);
+
+    await readFileLinkTooltip(page);
+    await leaveFileLink(page);
+    await readFileLinkTooltip(page);
+    await openLinkedFile(page);
+    await returnToAgent(page);
+    await readFileLinkTooltip(page);
+    await switchToFileTab(page);
+    await returnToAgent(page);
+    await readFileLinkTooltip(page);
+    await leaveFileLink(page);
+  } finally {
+    await agent.cleanup();
+  }
+});
diff --git a/packages/app/src/components/ui/tooltip.tsx b/packages/app/src/components/ui/tooltip.tsx
index ae00768a34..697a80fdcf 100644
--- a/packages/app/src/components/ui/tooltip.tsx
+++ b/packages/app/src/components/ui/tooltip.tsx
@@ -27,6 +27,7 @@ import { FadeIn, FadeOut } from "react-native-reanimated";
 import { StyleSheet } from "react-native-unistyles";
 import { useIsCompactFormFactor } from "@/constants/layout";
 import { FloatingSurface } from "@/components/ui/floating";
+import { useRetainedPanelActive } from "@/components/retained-panel";
 import { isNative, isWeb } from "@/constants/platform";
 import { getOverlayRoot, OVERLAY_Z } from "@/lib/overlay-root";
 
@@ -256,8 +257,15 @@ export function Tooltip({
   });
 
   const isCompact = useIsCompactFormFactor();
+  const active = useRetainedPanelActive();
   const opensOnPress = isNative || isCompact;
-  const enabled = opensOnPress ? enabledOnMobile : enabledOnDesktop;
+  const enabled = active && (opensOnPress ? enabledOnMobile : enabledOnDesktop);
+
+  // Remove the portal in the inactive commit, before the retained chat freezes.
+  // Closing also prevents the tooltip from returning when its panel is shown again.
+  useEffect(() => {
+    if (!active && isOpen) setIsOpen(false);
+  }, [active, isOpen, setIsOpen]);
 
   const value = useMemo<TooltipContextValue>(
     () => ({
@@ -329,6 +337,10 @@ export function TooltipTrigger({
     };
   }, [clearOpenTimer]);
 
+  useEffect(() => {
+    if (!ctx.enabled) clearOpenTimer();
+  }, [ctx.enabled, clearOpenTimer]);
+
   const handleHoverIn = useCallback(
     (e?: unknown) => {
       if (isCallable(onHoverIn)) onHoverIn(e);