diff --git a/apps/desktop/src/app/ClerkTokenStore.test.ts b/apps/desktop/src/app/ClerkTokenStore.test.ts
new file mode 100644
index 0000000000000..b7ac0e38d5142
--- /dev/null
+++ b/apps/desktop/src/app/ClerkTokenStore.test.ts
@@ -0,0 +1,189 @@
+// @effect-diagnostics nodeBuiltinImport:off -- These tests assert real POSIX modes on a temporary directory.
+import * as NodeFS from "node:fs";
+import * as NodeOS from "node:os";
+import * as NodePath from "node:path";
+import { assert, describe, it } from "@effect/vitest";
+import { vi } from "vite-plus/test";
+
+vi.mock("node:fs", { spy: true });
+
+import { openClerkTokenStorage, type ClerkTokenStorage } from "./ClerkTokenStore.ts";
+
+// oxlint-disable-next-line t3code/no-global-process-runtime -- Unix mode bits are the assertion; Windows reports them through ACLs.
+const describePosix = describe.skipIf(process.platform === "win32");
+
+const modeOf = (path: string): number => NodeFS.statSync(path).mode & 0o777;
+
+function writeLoose(path: string, contents: string): void {
+  NodeFS.writeFileSync(path, contents, { mode: 0o666 });
+  NodeFS.chmodSync(path, 0o666);
+}
+
+async function withStateDir(run: (stateDir: string) => Promise<void> | void): Promise<void> {
+  const stateDir = NodeFS.mkdtempSync(NodePath.join(NodeOS.tmpdir(), "t3-clerk-tokens-"));
+  try {
+    await run(stateDir);
+  } finally {
+    NodeFS.rmSync(stateDir, { recursive: true, force: true });
+  }
+}
+
+const idleStorage = (): ClerkTokenStorage => ({
+  getItem: async () => null,
+  setItem: async () => undefined,
+  removeItem: () => undefined,
+});
+
+describePosix("ClerkTokenStore", () => {
+  it("keeps clerk tokens at 0600 inside a 0700 directory", async () => {
+    await withStateDir(async (stateDir) => {
+      NodeFS.chmodSync(stateDir, 0o755);
+      const directory = NodePath.join(stateDir, "clerk");
+      const legacyPath = NodePath.join(stateDir, "clerk-tokens.json");
+      const tokenPath = NodePath.join(directory, "clerk-tokens.json");
+      NodeFS.mkdirSync(directory, { mode: 0o755 });
+      NodeFS.chmodSync(directory, 0o755);
+      writeLoose(legacyPath, '{"__clerk_client_jwt":"enc:existing"}\n');
+
+      const opened: string[] = [];
+      const storage = openClerkTokenStorage(stateDir, (cwd) => {
+        opened.push(cwd);
+        return {
+          getItem: async () => {
+            writeLoose(tokenPath, "from-get");
+            return "from-get";
+          },
+          setItem: (_key, value) => {
+            writeLoose(tokenPath, value);
+          },
+          removeItem: () => {
+            NodeFS.rmSync(tokenPath, { force: true });
+          },
+        };
+      });
+
+      assert.deepEqual(opened, [directory]);
+      assert.equal(modeOf(stateDir), 0o755);
+      assert.equal(modeOf(directory), 0o700);
+      assert.equal(modeOf(tokenPath), 0o600);
+      assert.equal(NodeFS.existsSync(legacyPath), false);
+      assert.equal(
+        NodeFS.readFileSync(tokenPath, "utf8"),
+        '{"__clerk_client_jwt":"enc:existing"}\n',
+      );
+
+      assert.equal(await storage.getItem("client"), "from-get");
+      assert.equal(modeOf(tokenPath), 0o600);
+      await storage.setItem("client", "from-set");
+      assert.equal(modeOf(tokenPath), 0o600);
+      assert.equal(NodeFS.readFileSync(tokenPath, "utf8"), "from-set");
+      storage.removeItem("client");
+      assert.equal(NodeFS.existsSync(tokenPath), false);
+
+      writeLoose(tokenPath, "kept");
+      writeLoose(legacyPath, "stale");
+      NodeFS.chmodSync(directory, 0o755);
+      openClerkTokenStorage(stateDir, () => idleStorage());
+      assert.equal(modeOf(directory), 0o700);
+      assert.equal(modeOf(tokenPath), 0o600);
+      assert.equal(NodeFS.existsSync(legacyPath), false);
+      assert.equal(NodeFS.readFileSync(tokenPath, "utf8"), "kept");
+    });
+  });
+
+  it("removes the legacy token file when the private copy already exists", async () => {
+    await withStateDir((stateDir) => {
+      const directory = NodePath.join(stateDir, "clerk");
+      const legacyPath = NodePath.join(stateDir, "clerk-tokens.json");
+      const tokenPath = NodePath.join(directory, "clerk-tokens.json");
+      NodeFS.mkdirSync(directory, { mode: 0o755 });
+      writeLoose(legacyPath, "stale-credential");
+      writeLoose(tokenPath, "kept-credential");
+
+      openClerkTokenStorage(stateDir, () => idleStorage());
+
+      assert.equal(NodeFS.existsSync(legacyPath), false);
+      assert.equal(modeOf(directory), 0o700);
+      assert.equal(modeOf(tokenPath), 0o600);
+      assert.equal(NodeFS.readFileSync(tokenPath, "utf8"), "kept-credential");
+    });
+  });
+
+  it("resolves a relative state directory before opening storage", async () => {
+    await withStateDir(async (stateDir) => {
+      const relativeStateDir = NodePath.relative(process.cwd(), stateDir);
+      const opened: string[] = [];
+      openClerkTokenStorage(relativeStateDir, (directory) => {
+        opened.push(directory);
+        return idleStorage();
+      });
+
+      const directory = NodePath.join(stateDir, "clerk");
+      assert.equal(NodePath.isAbsolute(relativeStateDir), false);
+      assert.deepEqual(opened, [directory]);
+      assert.equal(modeOf(directory), 0o700);
+    });
+  });
+
+  it("migrates relative state paths from Electron userData, not the working directory", async () => {
+    await withStateDir((stateDir) => {
+      const relativeStateDir = NodePath.relative(process.cwd(), stateDir);
+      const userData = NodePath.join(
+        stateDir,
+        "electron",
+        ...relativeStateDir.split(NodePath.sep).map(() => "profile"),
+      );
+      const legacyStateDir = NodePath.join(userData, relativeStateDir);
+      const legacyPath = NodePath.join(legacyStateDir, "clerk-tokens.json");
+      NodeFS.mkdirSync(legacyStateDir, { recursive: true });
+      writeLoose(legacyPath, "existing-session");
+      const unrelatedPath = NodePath.join(stateDir, "clerk-tokens.json");
+      writeLoose(unrelatedPath, "not-the-electron-session");
+
+      openClerkTokenStorage(relativeStateDir, idleStorage, userData);
+
+      const tokenPath = NodePath.join(stateDir, "clerk", "clerk-tokens.json");
+      assert.equal(NodeFS.readFileSync(tokenPath, "utf8"), "existing-session");
+      assert.equal(modeOf(tokenPath), 0o600);
+      assert.equal(NodeFS.existsSync(legacyPath), false);
+      assert.equal(NodeFS.readFileSync(unrelatedPath, "utf8"), "not-the-electron-session");
+    });
+  });
+
+  it("migrates tokens when the legacy directory is on another filesystem", async () => {
+    await withStateDir((stateDir) => {
+      const legacyPath = NodePath.join(stateDir, "clerk-tokens.json");
+      writeLoose(legacyPath, "existing-session");
+      using _rename = vi.spyOn(NodeFS, "renameSync").mockImplementation(() => {
+        throw Object.assign(new Error("cross-device link"), { code: "EXDEV" });
+      });
+
+      openClerkTokenStorage(stateDir, idleStorage);
+
+      const tokenPath = NodePath.join(stateDir, "clerk", "clerk-tokens.json");
+      assert.equal(NodeFS.readFileSync(tokenPath, "utf8"), "existing-session");
+      assert.equal(modeOf(tokenPath), 0o600);
+      assert.equal(NodeFS.existsSync(legacyPath), false);
+    });
+  });
+
+  it("does not follow a symlinked clerk directory or token file", async () => {
+    await withStateDir(async (stateDir) => {
+      const outsideDirectory = NodePath.join(stateDir, "outside-dir");
+      NodeFS.mkdirSync(outsideDirectory, { mode: 0o755 });
+      NodeFS.chmodSync(outsideDirectory, 0o755);
+      NodeFS.symlinkSync(outsideDirectory, NodePath.join(stateDir, "clerk"));
+
+      assert.throws(() => openClerkTokenStorage(stateDir, idleStorage), /must be a real directory/);
+      assert.equal(modeOf(outsideDirectory), 0o755);
+      NodeFS.unlinkSync(NodePath.join(stateDir, "clerk"));
+
+      const outsideFile = NodePath.join(stateDir, "outside.json");
+      NodeFS.writeFileSync(outsideFile, "secret", { mode: 0o644 });
+      NodeFS.chmodSync(outsideFile, 0o644);
+      NodeFS.symlinkSync(outsideFile, NodePath.join(stateDir, "clerk-tokens.json"));
+      assert.throws(() => openClerkTokenStorage(stateDir, idleStorage), /must be a regular file/);
+      assert.equal(modeOf(outsideFile), 0o644);
+    });
+  });
+});
diff --git a/apps/desktop/src/app/ClerkTokenStore.ts b/apps/desktop/src/app/ClerkTokenStore.ts
new file mode 100644
index 0000000000000..005736c97cb38
--- /dev/null
+++ b/apps/desktop/src/app/ClerkTokenStore.ts
@@ -0,0 +1,117 @@
+// @effect-diagnostics nodeBuiltinImport:off -- The Clerk bridge must lock the token file down before startup can yield to Electron's ready event.
+import * as NodeFS from "node:fs";
+import * as NodePath from "node:path";
+
+// electron-store chmods every write to 0666; the private directory protects tokens during writes.
+const CLERK_TOKEN_DIRECTORY_MODE = 0o700;
+const CLERK_TOKEN_FILE_MODE = 0o600;
+const CLERK_TOKEN_DIRECTORY_NAME = "clerk";
+const CLERK_TOKEN_FILE_NAME = "clerk-tokens.json";
+
+type Awaitable<T> = T | Promise<T>;
+
+export interface ClerkTokenStorage {
+  readonly getItem: (key: string) => Awaitable<string | null>;
+  readonly setItem: (key: string, value: string) => Awaitable<void>;
+  readonly removeItem: (key: string) => Awaitable<void>;
+}
+
+function isErrno(error: unknown, code: string): boolean {
+  return typeof error === "object" && error !== null && "code" in error && error.code === code;
+}
+
+function lstatIfExists(path: string): NodeFS.Stats | undefined {
+  try {
+    return NodeFS.lstatSync(path);
+  } catch (error) {
+    if (isErrno(error, "ENOENT")) return undefined;
+    throw error;
+  }
+}
+
+function assertRegularFile(path: string, stat: NodeFS.Stats): void {
+  if (stat.isSymbolicLink() || !stat.isFile()) {
+    throw new Error(`Clerk token file "${path}" must be a regular file.`);
+  }
+}
+
+function restrictClerkTokenFile(path: string): void {
+  const stat = lstatIfExists(path);
+  if (stat === undefined) return;
+  assertRegularFile(path, stat);
+  if ((stat.mode & 0o777) === CLERK_TOKEN_FILE_MODE) return;
+  NodeFS.chmodSync(path, CLERK_TOKEN_FILE_MODE);
+}
+
+function migrateLegacyClerkTokenFile(stateDir: string, directory: string): void {
+  const legacyPath = NodePath.join(stateDir, CLERK_TOKEN_FILE_NAME);
+  const tokenPath = NodePath.join(directory, CLERK_TOKEN_FILE_NAME);
+  const legacy = lstatIfExists(legacyPath);
+  if (legacy !== undefined) {
+    assertRegularFile(legacyPath, legacy);
+    NodeFS.chmodSync(legacyPath, CLERK_TOKEN_FILE_MODE);
+  }
+
+  const destination = lstatIfExists(tokenPath);
+  if (destination === undefined) {
+    if (legacy === undefined) return;
+    try {
+      NodeFS.copyFileSync(legacyPath, tokenPath, NodeFS.constants.COPYFILE_EXCL);
+      NodeFS.chmodSync(tokenPath, CLERK_TOKEN_FILE_MODE);
+      NodeFS.unlinkSync(legacyPath);
+    } catch (error) {
+      if (!isErrno(error, "ENOENT")) throw error;
+    }
+    return;
+  }
+
+  assertRegularFile(tokenPath, destination);
+  NodeFS.chmodSync(tokenPath, CLERK_TOKEN_FILE_MODE);
+  if (legacy === undefined) return;
+  try {
+    NodeFS.unlinkSync(legacyPath);
+  } catch (error) {
+    if (!isErrno(error, "ENOENT")) throw error;
+  }
+}
+
+function restrictAfter<T>(run: () => Awaitable<T>, tighten: () => void): Awaitable<T> {
+  let result: Awaitable<T>;
+  try {
+    result = run();
+  } catch (error) {
+    tighten();
+    throw error;
+  }
+  if (result instanceof Promise) return result.finally(tighten);
+  tighten();
+  return result;
+}
+
+/** Opens Clerk token storage in a private directory and keeps the file at `0600`. */
+export function openClerkTokenStorage(
+  stateDir: string,
+  createStorage: (directory: string) => ClerkTokenStorage,
+  userDataPath = ".",
+): ClerkTokenStorage {
+  const absoluteStateDir = NodePath.resolve(stateDir);
+  const directory = NodePath.join(absoluteStateDir, CLERK_TOKEN_DIRECTORY_NAME);
+  NodeFS.mkdirSync(directory, { recursive: true, mode: CLERK_TOKEN_DIRECTORY_MODE });
+  const stat = NodeFS.lstatSync(directory);
+  if (stat.isSymbolicLink() || !stat.isDirectory()) {
+    throw new Error(`Clerk token directory "${directory}" must be a real directory.`);
+  }
+  NodeFS.chmodSync(directory, CLERK_TOKEN_DIRECTORY_MODE);
+  // electron-store rebases relative paths under Electron userData, not the working directory.
+  migrateLegacyClerkTokenFile(NodePath.resolve(userDataPath, stateDir), directory);
+  const tokenPath = NodePath.join(directory, CLERK_TOKEN_FILE_NAME);
+  restrictClerkTokenFile(tokenPath);
+
+  const storage = createStorage(directory);
+  const tighten = () => restrictClerkTokenFile(tokenPath);
+  return {
+    getItem: (key) => restrictAfter(() => storage.getItem(key), tighten),
+    setItem: (key, value) => restrictAfter(() => storage.setItem(key, value), tighten),
+    removeItem: (key) => restrictAfter(() => storage.removeItem(key), tighten),
+  };
+}
diff --git a/apps/desktop/src/app/DesktopClerk.test.ts b/apps/desktop/src/app/DesktopClerk.test.ts
index 602383309be44..ca194ba8c5fa0 100644
--- a/apps/desktop/src/app/DesktopClerk.test.ts
+++ b/apps/desktop/src/app/DesktopClerk.test.ts
@@ -1,13 +1,21 @@
 // @effect-diagnostics nodeBuiltinImport:off globalFetchInEffect:off - Hosted handoff test uses a real localhost listener without an OpenAI account.
+import * as NodeFS from "node:fs";
 import * as NodeHttp from "node:http";
-import * as NodePath from "@effect/platform-node/NodePath";
+import * as NodeOS from "node:os";
+import * as NodePath from "node:path";
+import * as NodePathLayer from "@effect/platform-node/NodePath";
 import { codexAuthHandoffUrl, readCodexAuthDelivery } from "@t3tools/shared/codexAuthHandoff";
 import { EnvironmentId, ProviderInstanceId } from "@t3tools/contracts";
 import * as HostProcess from "@t3tools/shared/HostProcess";
 import { assert, describe, it } from "@effect/vitest";
 import * as Effect from "effect/Effect";
 import * as Layer from "effect/Layer";
-import { beforeEach, vi } from "vite-plus/test";
+import { afterAll, beforeEach, vi } from "vite-plus/test";
+
+const clerkStateDir = NodeFS.mkdtempSync(NodePath.join(NodeOS.tmpdir(), "t3-desktop-clerk-"));
+afterAll(() => {
+  NodeFS.rmSync(clerkStateDir, { recursive: true, force: true });
+});
 
 const { createClerkBridgeMock, requestSingleInstanceLockMock, storageAdapter, storageMock } =
   vi.hoisted(() => ({
@@ -60,7 +68,7 @@ const layerDesktopClerk = (
   isPackaged = false,
 ) => {
   const environment = DesktopEnvironment.DesktopEnvironment.of({
-    stateDir: "/tmp/t3-state",
+    stateDir: clerkStateDir,
     isDevelopment,
     appDataDirectory: "/tmp/app-data",
     platform,
@@ -96,7 +104,7 @@ const layerDesktopClerk = (
   return DesktopClerk.layer.pipe(
     Layer.provide(
       Layer.mergeAll(
-        NodePath.layerPosix,
+        NodePathLayer.layerPosix,
         Layer.succeed(DesktopEnvironment.DesktopEnvironment, environment),
         Layer.succeed(ElectronApp.ElectronApp, electronApp),
         Layer.succeed(ElectronShell.ElectronShell, shell),
@@ -199,6 +207,10 @@ describe("DesktopClerk", () => {
         "on:open-url",
         "createClerkBridge",
       ]);
+      assert.deepEqual(storageMock.mock.calls, [
+        [{ path: NodePath.join(NodePath.resolve(clerkStateDir), "clerk") }],
+      ]);
+      assert.notStrictEqual(createClerkBridgeMock.mock.calls[0]?.[0]?.storage, storageAdapter);
     },
   );
 
diff --git a/apps/desktop/src/app/DesktopClerk.ts b/apps/desktop/src/app/DesktopClerk.ts
index fd49354a048e4..2aa9726ee49f1 100644
--- a/apps/desktop/src/app/DesktopClerk.ts
+++ b/apps/desktop/src/app/DesktopClerk.ts
@@ -22,6 +22,7 @@ import * as ElectronProtocol from "../electron/ElectronProtocol.ts";
 import * as ElectronWindow from "../electron/ElectronWindow.ts";
 import * as DesktopUserData from "./DesktopUserData.ts";
 import * as DesktopEnvironment from "./DesktopEnvironment.ts";
+import { openClerkTokenStorage } from "./ClerkTokenStore.ts";
 import * as DesktopWebLinks from "./DesktopWebLinks.ts";
 
 declare const __T3CODE_BUILD_CLERK_PUBLISHABLE_KEY__: string | undefined;
@@ -85,9 +86,18 @@ export const desktopClerkFrontendApiHostname = resolveDesktopClerkFrontendApiHos
     : __T3CODE_BUILD_CLERK_PUBLISHABLE_KEY__,
 );
 
-function createDesktopClerkBridge(stateDir: string, isDevelopment: boolean, version: string) {
+function createDesktopClerkBridge(
+  stateDir: string,
+  isDevelopment: boolean,
+  version: string,
+  userDataPath: string,
+) {
   return createClerkBridge({
-    storage: storage({ path: stateDir }),
+    storage: openClerkTokenStorage(
+      stateDir,
+      (directory) => storage({ path: directory }),
+      userDataPath,
+    ),
     manageSingleInstanceLock: false,
     passkeys: true,
     renderer: {
@@ -137,6 +147,7 @@ export const make = Effect.gen(function* () {
           environment.stateDir,
           environment.isDevelopment,
           environment.appVersion,
+          userDataPath,
         ),
       catch: (cause) =>
         new DesktopClerkBridgeInitializationError({