diff --git a/apps/desktop/src/window/DesktopStatusIndicator.ts b/apps/desktop/src/window/DesktopStatusIndicator.ts
index 6828508a..e38e7d42 100644
--- a/apps/desktop/src/window/DesktopStatusIndicator.ts
+++ b/apps/desktop/src/window/DesktopStatusIndicator.ts
@@ -1,4 +1,8 @@
-import type { DesktopMenuActionPayload, DesktopTaskbarStatusInput } from "@threadlines/contracts";
+import type {
+  DesktopMenuActionPayload,
+  DesktopTaskbarStatusInput,
+  DesktopTaskbarThreadSummary,
+} from "@threadlines/contracts";
 import * as Cause from "effect/Cause";
 import * as Context from "effect/Context";
 import * as Effect from "effect/Effect";
@@ -128,6 +132,17 @@ function createDefaultStatus(): DesktopTaskbarStatusInput {
   return { status: "idle", description: "No active agent sessions" };
 }
 
+function describeThreadMenuState(state: DesktopTaskbarThreadSummary["state"]): string {
+  switch (state) {
+    case "running":
+      return "running";
+    case "waiting":
+      return "waiting on background tasks";
+    case "completed":
+      return "completed";
+  }
+}
+
 function truncateThreadMenuLabel(title: string): string {
   const trimmed = title.trim();
   if (trimmed.length === 0) {
@@ -324,7 +339,7 @@ const make = Effect.gen(function* () {
       .map((thread) => ({
         label: truncateThreadMenuLabel(thread.title),
         icon: thread.state === "completed" ? images.menuCompleted : images.menuRunning,
-        toolTip: `${thread.title.trim()} — ${thread.state === "completed" ? "completed" : "running"}`,
+        toolTip: `${thread.title.trim()} — ${describeThreadMenuState(thread.state)}`,
         click: () =>
           runTrayEffect(
             "open-thread",
diff --git a/apps/web/src/components/ChatView.tsx b/apps/web/src/components/ChatView.tsx
index 96d0a9bc..d286a74f 100644
--- a/apps/web/src/components/ChatView.tsx
+++ b/apps/web/src/components/ChatView.tsx
@@ -87,6 +87,7 @@ import {
   hasActionableProposedPlan,
   hasToolActivityForTurn,
   isLatestTurnSettled,
+  isWaitingOnBackgroundTasks,
   formatElapsed,
   type McpAuthReconnectAction,
   type ProviderAuthReconnectAction,
@@ -1404,8 +1405,10 @@ export default function ChatView(props: ChatViewProps) {
   const latestTurnSettled = isLatestTurnSettled(activeLatestTurn, activeThread?.session ?? null);
   // Same rule as the sidebar's "Background" pill: settled, but a provider
   // task will start the thread back up on its own.
-  const isWaitingOnBackgroundTasks =
-    latestTurnSettled && (activeThread?.session?.pendingBackgroundTaskCount ?? 0) > 0;
+  const waitingOnBackgroundTasks = isWaitingOnBackgroundTasks(
+    activeLatestTurn,
+    activeThread?.session ?? null,
+  );
   const activeProjectRef = activeThread
     ? scopeProjectRef(activeThread.environmentId, activeThread.projectId)
     : null;
@@ -6706,7 +6709,7 @@ export default function ChatView(props: ChatViewProps) {
               key={activeThread.id}
               emptyState={firstRunSetupEmptyState ?? draftTimelineEmptyState}
               isWorking={isWorking}
-              isWaitingOnBackgroundTasks={isWaitingOnBackgroundTasks}
+              isWaitingOnBackgroundTasks={waitingOnBackgroundTasks}
               activeStatusLabel={activeStatusLabel}
               activeTurnInProgress={isWorking || !latestTurnSettled}
               activeTurnId={activeLatestTurn?.turnId ?? null}
diff --git a/apps/web/src/components/Sidebar.logic.ts b/apps/web/src/components/Sidebar.logic.ts
index 20eadd35..9ef18197 100644
--- a/apps/web/src/components/Sidebar.logic.ts
+++ b/apps/web/src/components/Sidebar.logic.ts
@@ -8,7 +8,7 @@ import {
   type ThreadSortInput,
 } from "../lib/threadSort";
 import type { SidebarThreadSummary, Thread } from "../types";
-import { isLatestTurnSettled } from "../session-logic";
+import { isLatestTurnSettled, isWaitingOnBackgroundTasks } from "../session-logic";
 
 export const THREAD_SELECTION_SAFE_SELECTOR = "[data-thread-item], [data-thread-selection-safe]";
 export const THREAD_JUMP_HINT_SHOW_DELAY_MS = 100;
@@ -358,8 +358,7 @@ export function resolveThreadStatusPill(input: {
 
   // Settled turn with provider tasks still running: the provider will start
   // the thread back up on its own when they finish.
-  const pendingBackgroundTaskCount = thread.session?.pendingBackgroundTaskCount ?? 0;
-  if (pendingBackgroundTaskCount > 0 && isLatestTurnSettled(thread.latestTurn, thread.session)) {
+  if (isWaitingOnBackgroundTasks(thread.latestTurn, thread.session)) {
     return {
       label: "Background",
       colorClass: "text-cyan-600 dark:text-cyan-300/90",
diff --git a/apps/web/src/routes/__root.tsx b/apps/web/src/routes/__root.tsx
index 90d0d9a7..5b9cac68 100644
--- a/apps/web/src/routes/__root.tsx
+++ b/apps/web/src/routes/__root.tsx
@@ -53,6 +53,7 @@ import {
   useServerConfigUpdatedSubscription,
   useServerWelcomeSubscription,
 } from "../rpc/serverState";
+import { isWaitingOnBackgroundTasks } from "../session-logic";
 import { type AppState, selectRunningSidebarThreadsAcrossEnvironments, useStore } from "../store";
 import { useUiStateStore } from "../uiStateStore";
 import { syncBrowserChromeTheme } from "../hooks/useTheme";
@@ -193,7 +194,9 @@ function selectRunningTaskbarThreads(state: AppState): DesktopTaskbarThreadSumma
     threadId: thread.id,
     environmentId: thread.environmentId,
     title: thread.title,
-    state: "running" as const,
+    state: isWaitingOnBackgroundTasks(thread.latestTurn, thread.session)
+      ? ("waiting" as const)
+      : ("running" as const),
   }));
 }
 
diff --git a/apps/web/src/session-logic.ts b/apps/web/src/session-logic.ts
index 710ef1df..8368bc70 100644
--- a/apps/web/src/session-logic.ts
+++ b/apps/web/src/session-logic.ts
@@ -466,6 +466,23 @@ export function isLatestTurnSettled(
   return true;
 }
 
+type SessionBackgroundState = SessionLifecycleState &
+  Partial<Pick<ThreadSession, "pendingBackgroundTaskCount">>;
+
+/**
+ * The turn has settled but provider tasks (background subagents, deferred
+ * shell commands) are still running and will start the thread back up on
+ * their own. The thread is waiting, not finished, so it counts as live work
+ * everywhere the app counts it: sidebar pill, taskbar badge, quit and update
+ * warnings.
+ */
+export function isWaitingOnBackgroundTasks(
+  latestTurn: LatestTurnTiming | null,
+  session: SessionBackgroundState | null,
+): boolean {
+  return (session?.pendingBackgroundTaskCount ?? 0) > 0 && isLatestTurnSettled(latestTurn, session);
+}
+
 export function deriveActiveModelFallbackState(
   activities: ReadonlyArray<OrchestrationThreadActivity>,
   latestTurn: OrchestrationLatestTurn | null | undefined,
diff --git a/apps/web/src/store.test.ts b/apps/web/src/store.test.ts
index 1e2a91aa..26419c9b 100644
--- a/apps/web/src/store.test.ts
+++ b/apps/web/src/store.test.ts
@@ -28,12 +28,14 @@ import {
   selectThreadCheckout,
   setThreadBranch,
   selectThreadsAcrossEnvironments,
+  selectRunningSidebarThreadsAcrossEnvironments,
   type AppState,
   type EnvironmentState,
 } from "./store";
 import {
   DEFAULT_INTERACTION_MODE,
   DEFAULT_COMPOSER_RUNTIME_MODE,
+  type SidebarThreadSummary,
   type Thread,
   type ThreadSession,
 } from "./types";
@@ -1550,3 +1552,72 @@ describe("incremental orchestration updates", () => {
     expect(threadsOf(next)[0]?.latestTurn?.sourceProposedPlan).toBeUndefined();
   });
 });
+
+describe("selectRunningSidebarThreadsAcrossEnvironments", () => {
+  function makeSidebarSummary(
+    overrides: Partial<SidebarThreadSummary> & Pick<SidebarThreadSummary, "id">,
+  ): SidebarThreadSummary {
+    return {
+      environmentId: localEnvironmentId,
+      projectId: ProjectId.make("project-1"),
+      title: "Thread",
+      interactionMode: DEFAULT_INTERACTION_MODE,
+      session: null,
+      createdAt: "2026-02-13T00:00:00.000Z",
+      archivedAt: null,
+      pinnedAt: null,
+      doneOverride: null,
+      lastSeenAt: null,
+      latestTurn: null,
+      branch: null,
+      worktreePath: null,
+      effectiveCwd: null,
+      latestUserMessageAt: null,
+      hasPendingApprovals: false,
+      hasPendingUserInput: false,
+      hasActionableProposedPlan: false,
+      cumulativeDiffStat: null,
+      ...overrides,
+    };
+  }
+
+  it("keeps a settled thread live while background provider tasks are still running", () => {
+    const settledSession: ThreadSession = {
+      provider: ProviderDriverKind.make("claude"),
+      status: "ready",
+      orchestrationStatus: "ready",
+      checkoutCwd: "/tmp/project",
+      createdAt: "2026-02-13T00:00:00.000Z",
+      updatedAt: "2026-02-13T00:05:00.000Z",
+    };
+    const settledTurn = {
+      turnId: TurnId.make("turn-1"),
+      state: "completed" as const,
+      assistantMessageId: null,
+      requestedAt: "2026-02-13T00:00:00.000Z",
+      startedAt: "2026-02-13T00:00:00.000Z",
+      completedAt: "2026-02-13T00:05:00.000Z",
+    };
+    const waiting = makeSidebarSummary({
+      id: ThreadId.make("thread-waiting"),
+      session: { ...settledSession, pendingBackgroundTaskCount: 2 },
+      latestTurn: settledTurn,
+    });
+    const finished = makeSidebarSummary({
+      id: ThreadId.make("thread-finished"),
+      session: { ...settledSession, pendingBackgroundTaskCount: 0 },
+      latestTurn: settledTurn,
+    });
+    const state = makeEmptyState({
+      threadIds: [waiting.id, finished.id],
+      sidebarThreadSummaryById: {
+        [waiting.id]: waiting,
+        [finished.id]: finished,
+      },
+    });
+
+    expect(selectRunningSidebarThreadsAcrossEnvironments(state).map((thread) => thread.id)).toEqual(
+      [waiting.id],
+    );
+  });
+});
diff --git a/apps/web/src/store.ts b/apps/web/src/store.ts
index cb919bda..fb2d9678 100644
--- a/apps/web/src/store.ts
+++ b/apps/web/src/store.ts
@@ -50,6 +50,7 @@ import {
   derivePendingUserInputs,
   findLatestProposedPlan,
   hasActionableProposedPlan,
+  isWaitingOnBackgroundTasks,
   sumTurnDiffStats,
 } from "./session-logic";
 import { getThreadFromEnvironmentState } from "./threadDerivation";
@@ -2198,13 +2199,21 @@ export function selectSidebarThreadsAcrossEnvironments(state: AppState): Sidebar
   );
 }
 
-/** Sidebar threads whose agent session is running right now, across every environment. */
+/**
+ * Sidebar threads with live agent work, across every environment: the session
+ * is running a turn, or the turn settled and background provider tasks
+ * (subagents, deferred commands) will start it back up on their own. Drives the
+ * taskbar badge and the quit and update warnings, so a thread that is only
+ * waiting on its subagents must not read as finished here.
+ */
 export function selectRunningSidebarThreadsAcrossEnvironments(
   state: AppState,
 ): SidebarThreadSummary[] {
   return selectSidebarThreadsAcrossEnvironments(state).filter(
     (thread) =>
-      thread.session?.status === "running" || thread.session?.orchestrationStatus === "running",
+      thread.session?.status === "running" ||
+      thread.session?.orchestrationStatus === "running" ||
+      isWaitingOnBackgroundTasks(thread.latestTurn, thread.session),
   );
 }
 
diff --git a/packages/contracts/src/ipc.ts b/packages/contracts/src/ipc.ts
index ea908b64..cb5d0618 100644
--- a/packages/contracts/src/ipc.ts
+++ b/packages/contracts/src/ipc.ts
@@ -367,9 +367,10 @@ export const DesktopUpdateCheckResultSchema = Schema.Struct({
   state: DesktopUpdateStateSchema,
 });
 
-export type DesktopTaskbarThreadState = "running" | "completed";
+/** "waiting": the turn settled but background provider tasks keep the thread live. */
+export type DesktopTaskbarThreadState = "running" | "waiting" | "completed";
 
-export const DesktopTaskbarThreadStateSchema = Schema.Literals(["running", "completed"]);
+export const DesktopTaskbarThreadStateSchema = Schema.Literals(["running", "waiting", "completed"]);
 
 /** A thread surfaced in the desktop status item menu (click-to-open). */
 export interface DesktopTaskbarThreadSummary {