diff --git a/apps/server/src/storageCleanup.test.ts b/apps/server/src/storageCleanup.test.ts
index 5f945abd1858c..6d87a03e55a76 100644
--- a/apps/server/src/storageCleanup.test.ts
+++ b/apps/server/src/storageCleanup.test.ts
@@ -112,14 +112,16 @@ describe("V2 storage cleanup eligibility", () => {
   const candidate = () => shell({ branch: "feature", worktreePath: "/worktrees/feature" });
 
   it("allows an idle worktree and rejects the project checkout", () => {
-    expect(storageCleanupThreadIdle(candidate(), NOW_MS)).toBe(true);
-    expect(storageCleanupThreadIdle(shell(), NOW_MS)).toBe(false);
+    expect(storageCleanupThreadIdle(candidate(), NOW_MS, DEFAULT_SERVER_SETTINGS)).toBe(true);
+    expect(storageCleanupThreadIdle(shell(), NOW_MS, DEFAULT_SERVER_SETTINGS)).toBe(false);
   });
 
   it.each(["running", "starting", "preparing", "waiting", "queued"] as const)(
     "retains a worktree while its thread is %s",
     (status) => {
-      expect(storageCleanupThreadIdle(candidateWithStatus(status), NOW_MS)).toBe(false);
+      expect(
+        storageCleanupThreadIdle(candidateWithStatus(status), NOW_MS, DEFAULT_SERVER_SETTINGS),
+      ).toBe(false);
     },
   );
 
@@ -133,6 +135,7 @@ describe("V2 storage cleanup eligibility", () => {
             pendingBackgroundTasks: [{ taskId: "task-1", kind: "command" }],
           },
           NOW_MS,
+          DEFAULT_SERVER_SETTINGS,
         ),
       ).toBe(false);
     },
@@ -152,6 +155,7 @@ describe("V2 storage cleanup eligibility", () => {
             },
           },
           NOW_MS,
+          DEFAULT_SERVER_SETTINGS,
         ),
       ).toBe(false);
     },
@@ -159,16 +163,83 @@ describe("V2 storage cleanup eligibility", () => {
 
   it("retains an active run even if the shell status is idle", () => {
     expect(
-      storageCleanupThreadIdle({ ...candidate(), activeRunId: RunId.make("run") }, NOW_MS),
+      storageCleanupThreadIdle(
+        { ...candidate(), activeRunId: RunId.make("run") },
+        NOW_MS,
+        DEFAULT_SERVER_SETTINGS,
+      ),
     ).toBe(false);
   });
 
   it("retains a queued prompt before the new run has been projected", () => {
     expect(
-      storageCleanupThreadIdle({ ...candidate(), latestUserMessageAt: at(-1_000) }, NOW_MS),
+      storageCleanupThreadIdle(
+        { ...candidate(), latestUserMessageAt: at(-1_000) },
+        NOW_MS,
+        DEFAULT_SERVER_SETTINGS,
+      ),
     ).toBe(false);
   });
 
+  it.each([
+    { name: "snoozed until a future reset", snooze: true, resetIn: DAY_MS, idle: false },
+    { name: "set to auto-resume", autoResume: true, resetIn: DAY_MS, idle: false },
+    { name: "with recovery turned off", resetIn: DAY_MS, idle: true },
+    { name: "auto-resuming after the reset", autoResume: true, resetIn: -1_000, idle: false },
+    { name: "snoozed past its reset", snooze: true, resetIn: -1_000, idle: true },
+    {
+      name: "settled with an auto-resume pending",
+      autoResume: true,
+      settled: true,
+      resetIn: -1_000,
+      idle: true,
+    },
+    { name: "not yet armed by the recovery worker", armed: false, resetIn: DAY_MS, idle: false },
+    {
+      name: "not yet armed, auto-resume after reset",
+      armed: false,
+      autoResumeSetting: true,
+      resetIn: -1_000,
+      idle: false,
+    },
+    {
+      name: "not armed with recovery settings off",
+      armed: false,
+      settingsOff: true,
+      resetIn: DAY_MS,
+      idle: true,
+    },
+  ])(
+    "treats a usage-limited thread $name as idle: $idle",
+    ({
+      autoResume = false,
+      snooze = false,
+      armed = true,
+      autoResumeSetting = false,
+      settled,
+      settingsOff,
+      resetIn,
+      idle,
+    }) => {
+      const runId = RunId.make("run-1");
+      const resetAt = DateTime.formatIso(at(resetIn));
+      expect(
+        storageCleanupThreadIdle(
+          {
+            ...candidateWithStatus("failed"),
+            latestRunId: runId,
+            lastErrorClass: "usage_limit",
+            usageLimitResetAt: resetAt,
+            settledOverride: settled ? "settled" : null,
+            limitRecovery: armed ? { runId, resetAt, autoResume, snooze } : null,
+          },
+          NOW_MS,
+          { autoResumeLimitedThreads: autoResumeSetting, snoozeLimitedThreads: !settingsOff },
+        ),
+      ).toBe(idle);
+    },
+  );
+
   it("uses V2 run activity instead of metadata refreshes for retention", () => {
     const thread = candidate();
     const runTime = at(-3 * DAY_MS);
@@ -2211,6 +2282,33 @@ describe("storage cleanup reports and local file policies", () => {
 });
 
 describe("settled worktree rechecks", () => {
+  it.live.each(["autoResumeLimitedThreads", "snoozeLimitedThreads"] as const)(
+    "keeps a usage-limited checkout when %s is enabled during measurement",
+    (preference) =>
+      runCleanupTest(
+        Effect.gen(function* () {
+          const fixture = yield* pausedMeasurementFixture();
+          fixture.setSettings({ autoResumeLimitedThreads: false, snoozeLimitedThreads: false });
+          fixture.setThreads([
+            shell({
+              branch: "feature",
+              worktreePath: fixture.worktree,
+              status: "failed",
+              latestRunId: RunId.make("limited-run"),
+              lastErrorClass: "usage_limit",
+              usageLimitResetAt: DateTime.formatIso(at(DAY_MS)),
+            }),
+          ]);
+          const run = yield* fixture.service.runNow.pipe(Effect.forkChild);
+          yield* Deferred.await(fixture.measuring);
+          fixture.setSettings({ [preference]: true });
+          yield* Deferred.succeed(fixture.resume, undefined);
+          const report = yield* Fiber.join(run);
+          expect(report.entries[0]?.outcome).toBe("kept");
+          expect(yield* fixture.fs.exists(fixture.worktree)).toBe(true);
+        }),
+      ),
+  );
   it.live.each([{ settledAt: null }, { settledAt: at(DAY_MS) }])(
     "keeps a checkout changed during measurement (%j)",
     (change) =>
diff --git a/apps/server/src/storageCleanup.ts b/apps/server/src/storageCleanup.ts
index 48154835e7bb4..deffe41cec571 100644
--- a/apps/server/src/storageCleanup.ts
+++ b/apps/server/src/storageCleanup.ts
@@ -115,7 +115,16 @@ function sameProjectWorktreePolicies(left: ServerSettings, right: ServerSettings
   );
 }
 
-export function storageCleanupThreadIdle(thread: OrchestrationV2ThreadShell, now: number): boolean {
+type LimitRecoverySettings = Pick<
+  ServerSettings,
+  "autoResumeLimitedThreads" | "snoozeLimitedThreads"
+>;
+
+export function storageCleanupThreadIdle(
+  thread: OrchestrationV2ThreadShell,
+  now: number,
+  settings: LimitRecoverySettings,
+): boolean {
   return (
     thread.worktreePath !== null &&
     thread.activeRunId === null &&
@@ -127,10 +136,41 @@ export function storageCleanupThreadIdle(thread: OrchestrationV2ThreadShell, now
       thread.status === "rolled_back") &&
     (thread.pendingBackgroundTasks?.length ?? 0) === 0 &&
     thread.pendingRuntimeRequest === null &&
-    !threadHasQueuedTurnStart(thread, now)
+    !threadHasQueuedTurnStart(thread, now) &&
+    !heldForLimitRecovery(thread, now, settings)
   );
 }
 
+// A run held for its usage-limit reset has its work still ahead of it, and a
+// fresh worktree would otherwise look unchanged and be removed before it runs.
+function heldForLimitRecovery(
+  thread: OrchestrationV2ThreadShell,
+  now: number,
+  settings: LimitRecoverySettings,
+): boolean {
+  if (
+    thread.status !== "failed" ||
+    thread.lastErrorClass !== "usage_limit" ||
+    !thread.usageLimitResetAt ||
+    thread.archivedAt !== null ||
+    thread.settledOverride === "settled"
+  )
+    return false;
+  const resetMs = Date.parse(thread.usageLimitResetAt);
+  const recovery = thread.limitRecovery;
+  if (recovery?.runId === thread.latestRunId && recovery.resetAt === thread.usageLimitResetAt)
+    // An auto-resume holds until its continuation replaces the failed run.
+    return recovery.autoResume || (recovery.snooze === true && resetMs > now);
+  // The recovery worker arms this failure on a later tick; hold it until then.
+  // Like the worker, skip a reset that had already passed when the run ended.
+  if (
+    !Number.isFinite(resetMs) ||
+    resetMs <= DateTime.toEpochMillis(thread.latestRunCompletedAt ?? thread.updatedAt)
+  )
+    return false;
+  return settings.autoResumeLimitedThreads || (settings.snoozeLimitedThreads && resetMs > now);
+}
+
 /** PR metadata refreshes must not reset the inactivity clock. */
 export function storageCleanupActivityAt(thread: OrchestrationV2ThreadShell): number {
   return Math.max(
@@ -799,7 +839,7 @@ const make = Effect.gen(function* () {
         if (project === undefined) return keep("project is unavailable");
         if (
           thread.branch === null ||
-          !group.every((member) => storageCleanupThreadIdle(member, now))
+          !group.every((member) => storageCleanupThreadIdle(member, now, serverSettings))
         )
           return keep(waitForStop("thread is running or has pending work"));
         if (group.some((member) => member.branch !== thread.branch))
@@ -968,7 +1008,7 @@ const make = Effect.gen(function* () {
                 shell.branch !== thread.branch ||
                 !Equal.equals(shell.settledAt, previous.settledAt) ||
                 (shell.settledAt !== null && !Equal.equals(shell.updatedAt, previous.updatedAt)) ||
-                !storageCleanupThreadIdle(shell, now) ||
+                !storageCleanupThreadIdle(shell, now, serverSettings) ||
                 path.resolve(shell.worktreePath!) !== worktreePath ||
                 storageCleanupActivityAt(shell) !== storageCleanupActivityAt(previous)
               );
@@ -1008,11 +1048,11 @@ const make = Effect.gen(function* () {
           return keep("commit changed since check");
         const finalChanges = yield* localChangesReason(worktreePath, settings);
         if (finalChanges !== null) return keep(finalChanges);
-        const current = resolveWorktreeCleanup(
-          yield* settingsService.getSettings,
-          thread.projectId,
-        );
+        const currentSettings = yield* settingsService.getSettings;
+        const current = resolveWorktreeCleanup(currentSettings, thread.projectId);
         if (
+          currentSettings.autoResumeLimitedThreads !== serverSettings.autoResumeLimitedThreads ||
+          currentSettings.snoozeLimitedThreads !== serverSettings.snoozeLimitedThreads ||
           Object.keys(settings).some(
             (key) =>
               current[key as keyof typeof settings] !== settings[key as keyof typeof settings],