diff --git a/cli/src/__tests__/install-command.test.ts b/cli/src/__tests__/install-command.test.ts
index c8292de7d6d..46bc6d73a4f 100644
--- a/cli/src/__tests__/install-command.test.ts
+++ b/cli/src/__tests__/install-command.test.ts
@@ -4,7 +4,16 @@ import path from "node:path";
 import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
 import { installCommand, resolveNpmInstallRequest } from "../commands/install.js";
 import { uninstallCommand } from "../commands/uninstall.js";
-import { readInstallManifest, resolveInstallStorePaths } from "../install-store.js";
+import {
+  INSTALL_MANIFEST_VERSION,
+  flipCurrentAtomic,
+  initializeInstallStore,
+  payloadPathFor,
+  readInstallManifest,
+  resolveInstallStorePaths,
+  withInstallStoreLock,
+  writeInstallManifestAtomic,
+} from "../install-store.js";
 import { resolveCliVersion } from "../version.js";
 
 const ORIGINAL_ENV = { ...process.env };
@@ -108,4 +117,29 @@ describe("managed install commands", () => {
     await expect(uninstallCommand()).rejects.toThrow("unverified install store");
     expect(fs.readFileSync(unrelatedFile, "utf8")).toBe("keep");
   });
+
+  it("refuses to uninstall while another store mutation holds the lock", async () => {
+    const paths = resolveInstallStorePaths();
+    const payloadPath = payloadPathFor(paths, "npm", "2026.720.0");
+    initializeInstallStore(paths);
+    fs.mkdirSync(payloadPath, { recursive: true });
+    flipCurrentAtomic(payloadPath, paths);
+    writeInstallManifestAtomic({
+      schemaVersion: INSTALL_MANIFEST_VERSION,
+      source: "npm",
+      version: "2026.720.0",
+      channel: "latest",
+      payloadPath,
+      installedAt: "2026-07-22T18:00:00.000Z",
+      previous: [],
+    }, paths);
+
+    await withInstallStoreLock(
+      async () => {
+        await expect(uninstallCommand()).rejects.toThrow("already running");
+      },
+      paths,
+    );
+    expect(fs.existsSync(paths.lockPath)).toBe(false);
+  });
 });
diff --git a/cli/src/commands/uninstall.ts b/cli/src/commands/uninstall.ts
index c1dc4eba027..ab8f9c76b06 100644
--- a/cli/src/commands/uninstall.ts
+++ b/cli/src/commands/uninstall.ts
@@ -6,18 +6,24 @@ import {
   removeManagedPathBlock,
   removeManagedShim,
   resolveInstallStorePaths,
+  withInstallStoreLock,
 } from "../install-store.js";
 
 export async function uninstallCommand(): Promise<void> {
   const paths = resolveInstallStorePaths();
-  if (fs.existsSync(paths.cliRoot)) assertManagedInstallStore(paths);
-  const shimRemoved = removeManagedShim(paths);
-  fs.rmSync(paths.cliRoot, { recursive: true, force: true });
+  const hadStore = fs.existsSync(paths.cliRoot);
+  if (hadStore) assertManagedInstallStore(paths);
+  const shimRemoved = await withInstallStoreLock(async () => {
+    if (hadStore) assertManagedInstallStore(paths);
+    const removed = removeManagedShim(paths);
 
-  const home = process.env.HOME;
-  for (const rcFile of home ? [path.join(home, ".bashrc"), path.join(home, ".zshrc")] : []) {
-    removeManagedPathBlock(rcFile);
-  }
+    const home = process.env.HOME;
+    for (const rcFile of home ? [path.join(home, ".bashrc"), path.join(home, ".zshrc")] : []) {
+      removeManagedPathBlock(rcFile);
+    }
+    fs.rmSync(paths.cliRoot, { recursive: true, force: true });
+    return removed;
+  }, paths, { initialize: !hadStore });
 
   if (!shimRemoved) {
     console.log(pc.yellow(`Left ${paths.shimPath} unchanged because it is not a Paperclip-managed shim.`));
diff --git a/cli/src/install-store.ts b/cli/src/install-store.ts
index 164376b5341..390a414dbc4 100644
--- a/cli/src/install-store.ts
+++ b/cli/src/install-store.ts
@@ -156,8 +156,9 @@ function processIsAlive(pid: number): boolean {
 export async function withInstallStoreLock<T>(
   callback: () => Promise<T>,
   paths = resolveInstallStorePaths(),
+  options: { initialize?: boolean } = {},
 ): Promise<T> {
-  initializeInstallStore(paths);
+  if (options.initialize !== false) initializeInstallStore(paths);
   const token = `${process.pid}:${Date.now()}:${Math.random().toString(16).slice(2)}`;
   const acquire = (): void => {
     const temporaryPath = `${paths.lockPath}.${token}.tmp`;