diff --git a/apps/server/src/storageCleanup.test.ts b/apps/server/src/storageCleanup.test.ts
index de1ccfefcf64f..303c0de822517 100644
--- a/apps/server/src/storageCleanup.test.ts
+++ b/apps/server/src/storageCleanup.test.ts
@@ -2322,6 +2322,35 @@ describe("storage cleanup reports and local file policies", () => {
       }),
     ),
   );
+  it.live("removes a worktree owned by a repository other than the project root", () =>
+    runCleanupTest(
+      Effect.gen(function* () {
+        const fixture = yield* cleanupFixture();
+        const { fs, command, config } = fixture;
+        const oldRepo = yield* fs.realPath(
+          yield* fs.makeTempDirectoryScoped({ prefix: "cleanup-old-repo-" }),
+        );
+        yield* command(oldRepo, ["init", "-b", "main"]);
+        yield* command(oldRepo, ["config", "user.email", "cleanup@example.test"]);
+        yield* command(oldRepo, ["config", "user.name", "Cleanup test"]);
+        yield* fs.writeFileString(`${oldRepo}/tracked.txt`, "original\n");
+        yield* command(oldRepo, ["add", "."]);
+        yield* command(oldRepo, ["commit", "-m", "initial"]);
+        yield* fs.makeDirectory(`${config.worktreesDir}/old-repo`, { recursive: true });
+        const oldWorktree = `${config.worktreesDir}/old-repo/feature`;
+        yield* command(oldRepo, ["worktree", "add", "-b", "feature", oldWorktree]);
+        fixture.setThreads([shell({ branch: "feature", worktreePath: oldWorktree })]);
+        const report = yield* fixture.service.runNow;
+        expect(report.entries.find((entry) => entry.path === oldWorktree)).toMatchObject({
+          outcome: "removed",
+        });
+        expect(yield* fs.exists(oldWorktree)).toBe(false);
+        expect((yield* command(oldRepo, ["worktree", "list", "--porcelain"])).stdout).not.toContain(
+          oldWorktree,
+        );
+      }),
+    ),
+  );
   it.live.each([
     [
       "its owner's branch is cleared",
diff --git a/apps/server/src/storageCleanup.ts b/apps/server/src/storageCleanup.ts
index a5f9cd7eefa12..6df5c6d6fbe7e 100644
--- a/apps/server/src/storageCleanup.ts
+++ b/apps/server/src/storageCleanup.ts
@@ -637,6 +637,21 @@ const make = Effect.gen(function* () {
     return (name?.startsWith("(") ? null : name) !== branch;
   });
 
+  // A worktree can outlive its project moving to another clone. Git removes a
+  // worktree through the repository that registered it, not through the
+  // project's current checkout, so resolve the owning repository first.
+  const worktreeRepository = Effect.fn("StorageCleanup.worktreeRepository")(function* (
+    worktreePath: string,
+  ) {
+    const commonDir = yield* git.execute({
+      operation: "StorageCleanup.worktreeRepository",
+      cwd: worktreePath,
+      args: ["rev-parse", "--git-common-dir"],
+    });
+    const resolved = path.resolve(worktreePath, commonDir.stdout.trim());
+    return path.basename(resolved) === ".git" ? path.dirname(resolved) : resolved;
+  });
+
   const localChangesReason = Effect.fn("StorageCleanup.localChangesReason")(function* (
     cwd: string,
     rules: WorktreeCleanupRules,
@@ -1215,14 +1230,15 @@ const make = Effect.gen(function* () {
               const changes = yield* localChangesReason(worktreePath, settings);
               if (changes !== null) return keep(changes);
             }
+            const repository = yield* worktreeRepository(worktreePath);
             yield* removeLinkedWorktree({
               operation: "StorageCleanup.cleanupGit",
-              cwd: project.workspaceRoot,
+              cwd: repository,
               worktreePath,
               // Git requires force for submodules; recursive checks above cannot make removal atomic.
               force: submodules.force,
               execute: git.execute,
-              run: (args) => cleanupGit(project.workspaceRoot, [...args], "git worktree remove"),
+              run: (args) => cleanupGit(repository, [...args], "git worktree remove"),
             });
             entries.push({ ...entry, outcome: "removed", reason: sentence(removalReason), bytes });
             yield* gitManager.invalidateStatus(project.workspaceRoot);