diff --git a/apps/server/src/storageCleanup.test.ts b/apps/server/src/storageCleanup.test.ts
index c05d4aed4cfbf..3fe2052830118 100644
--- a/apps/server/src/storageCleanup.test.ts
+++ b/apps/server/src/storageCleanup.test.ts
@@ -1198,6 +1198,71 @@ describe("orphan worktree reports", () => {
     ),
   );
 
+  it.live("reports linked worktrees nested deeper inside a plain folder", () =>
+    runCleanupTest(
+      Effect.gen(function* () {
+        const fixture = yield* cleanupFixture();
+        fixture.setThreads([]);
+        const replay = `${fixture.config.worktreesDir}/repository/replay`;
+        const deep = `${fixture.config.worktreesDir}/repository/deep`;
+        const worktrees = [`${deep}/a/b`, `${replay}/1376`];
+        for (const [index, worktree] of worktrees.entries()) {
+          yield* fixture.command(fixture.repo, [
+            "worktree",
+            "add",
+            "-b",
+            `nested-${index}`,
+            worktree,
+          ]);
+        }
+        for (const folder of [...worktrees, `${deep}/a`, deep, replay]) {
+          yield* fixture.fs.utimes(folder, 1, 1);
+        }
+        const report = yield* fixture.service.runNow;
+        expect(
+          report.entries
+            .map((entry) => ({ path: entry.path, reason: entry.reason }))
+            .sort((left, right) => String(left.path).localeCompare(String(right.path))),
+        ).toEqual(worktrees.map((path) => ({ path, reason: "No thread uses this worktree" })));
+      }),
+    ),
+  );
+
+  it.live("still reports a plain folder whose nested worktree registration is stale", () =>
+    runCleanupTest(
+      Effect.gen(function* () {
+        const fixture = yield* cleanupFixture();
+        fixture.setThreads([]);
+        const replay = `${fixture.config.worktreesDir}/repository/replay`;
+        const worktree = `${replay}/1376`;
+        yield* fixture.command(fixture.repo, ["worktree", "add", "-b", "locked", worktree]);
+        yield* fixture.command(fixture.repo, ["worktree", "lock", worktree]);
+        yield* fixture.fs.rename(worktree, `${replay}/moved`);
+        yield* fixture.fs.makeDirectory(worktree);
+        yield* fixture.fs.utimes(replay, 1, 1);
+        expect((yield* fixture.service.runNow).entries.map((entry) => entry.path)).toEqual([
+          replay,
+        ]);
+      }),
+    ),
+  );
+
+  it.live("does not report nested worktrees inside a project checkout", () =>
+    runCleanupTest(
+      Effect.gen(function* () {
+        const fixture = yield* cleanupFixture();
+        fixture.setThreads([]);
+        const project = `${fixture.config.worktreesDir}/repository/replay/project`;
+        const worktree = `${project}/nested`;
+        yield* fixture.fs.makeDirectory(project, { recursive: true });
+        fixture.setProjectRoots([fixture.repo, project]);
+        yield* fixture.command(fixture.repo, ["worktree", "add", "-b", "nested", worktree]);
+        for (const folder of [worktree, project]) yield* fixture.fs.utimes(folder, 1, 1);
+        expect((yield* fixture.service.runNow).entries).toEqual([]);
+      }),
+    ),
+  );
+
   it.live("continues after an inaccessible directory's git probe", (context) =>
     runCleanupTest(
       Effect.gen(function* () {
diff --git a/apps/server/src/storageCleanup.ts b/apps/server/src/storageCleanup.ts
index 526aaffa2abb3..a601d48ad82b1 100644
--- a/apps/server/src/storageCleanup.ts
+++ b/apps/server/src/storageCleanup.ts
@@ -452,6 +452,26 @@ const make = Effect.gen(function* () {
       },
       Effect.orElseSucceed(() => undefined),
     );
+    // Linked worktrees can sit deeper inside a plain folder, like <repository>/replay/<n>. Ask
+    // the projects' Git for them rather than walking folders that may hold large non-git trees.
+    let registered: ReadonlyArray<string> | undefined;
+    const nestedWorktrees = Effect.fnUntraced(function* (folder: string, managedRoot: string) {
+      if (yield* fs.exists(path.join(folder, ".git"))) return [];
+      registered ??= (yield* Effect.forEach(new Set(projectRoots), (root) =>
+        git.listWorktreePaths(root).pipe(Effect.orElseSucceed((): string[] => [])),
+      )).flat();
+      // Locked registrations outlive their directory, whose path may since hold something else.
+      return yield* Effect.filter(
+        registered.filter(
+          (worktree) => inside(folder, worktree) && !inProject(worktree, managedRoot),
+        ),
+        (worktree) =>
+          Effect.gen(function* () {
+            if (pathKey(yield* fs.realPath(worktree)) !== pathKey(worktree)) return false;
+            return (yield* fs.stat(path.join(worktree, ".git"))).type === "File";
+          }).pipe(Effect.orElseSucceed(() => false)),
+      );
+    });
     for (const root of roots) {
       // Worktrees can be <root>/<repository>/<branch> or explicitly <root>/<name>.
       for (const projectDirectory of yield* directories(root, root)) {
@@ -463,7 +483,8 @@ const make = Effect.gen(function* () {
             return;
           }
           for (const worktreePath of yield* directories(projectDirectory, root)) {
-            yield* report(worktreePath);
+            const nested = yield* nestedWorktrees(worktreePath, root);
+            for (const target of nested.length > 0 ? nested : [worktreePath]) yield* report(target);
           }
         }).pipe(Effect.orElseSucceed(() => undefined));
       }