diff --git a/package.json b/package.json
index e6442a0535..85f4ea931b 100644
--- a/package.json
+++ b/package.json
@@ -130,7 +130,7 @@
     "fallow:baseline": "fallow dead-code --save-baseline fallow-baselines/dead-code.json --summary && fallow health --report-only --save-baseline fallow-baselines/health.json --summary",
     "check:fallow": "fallow audit",
     "check:affected": "node --experimental-strip-types scripts/check-affected/run.ts",
-    "check:affected:test": "node --experimental-strip-types scripts/node-test-tmpdir.ts --experimental-strip-types --test scripts/check-affected/model.test.ts scripts/check-affected/platform-packages.test.ts scripts/check-affected/device-lanes.test.ts scripts/check-affected/run.test.ts",
+    "check:affected:test": "node --experimental-strip-types scripts/node-test-tmpdir.ts --experimental-strip-types --test scripts/check-affected/model.test.ts scripts/check-affected/platform-packages.test.ts scripts/check-affected/device-lanes.test.ts scripts/check-affected/lockfile-install-sync.test.ts scripts/check-affected/run.test.ts",
     "gate": "node --experimental-strip-types scripts/gate/run.ts",
     "check:gate-manifest": "node --experimental-strip-types scripts/gate/check.ts",
     "check:gate-manifest:test": "node --experimental-strip-types scripts/node-test-tmpdir.ts --experimental-strip-types --test scripts/gate/*.test.ts",
diff --git a/scripts/check-affected/lockfile-install-sync.test.ts b/scripts/check-affected/lockfile-install-sync.test.ts
new file mode 100644
index 0000000000..da6076bf12
--- /dev/null
+++ b/scripts/check-affected/lockfile-install-sync.test.ts
@@ -0,0 +1,85 @@
+import assert from 'node:assert/strict';
+import fs from 'node:fs';
+import path from 'node:path';
+import { test } from 'node:test';
+import { mkdtempForTestSync } from '../../src/__tests__/test-utils/tmp-dir.ts';
+import { checkLockfileInstallSync } from './lockfile-install-sync.ts';
+
+function writeLockfile(root: string, content: string): void {
+  fs.writeFileSync(path.join(root, 'pnpm-lock.yaml'), content);
+}
+
+function writeInstalledSnapshot(root: string, content: string): void {
+  const dir = path.join(root, 'node_modules', '.pnpm');
+  fs.mkdirSync(dir, { recursive: true });
+  fs.writeFileSync(path.join(dir, 'lock.yaml'), content);
+}
+
+test('reports in sync when the installed snapshot byte-matches the checked-out lockfile', () => {
+  const root = mkdtempForTestSync('agent-device-lockfile-sync-match-');
+  writeLockfile(root, 'lockfileVersion: 9.0\nimporters:\n  .: {}\n');
+  writeInstalledSnapshot(root, 'lockfileVersion: 9.0\nimporters:\n  .: {}\n');
+
+  assert.deepEqual(checkLockfileInstallSync(root), { status: 'in-sync' });
+});
+
+test('reports stale when the installed snapshot content differs from the checked-out lockfile', () => {
+  const root = mkdtempForTestSync('agent-device-lockfile-sync-stale-');
+  writeLockfile(
+    root,
+    'lockfileVersion: 9.0\nimporters:\n  .:\n    dependencies:\n      newDep: 1.0.0\n',
+  );
+  writeInstalledSnapshot(root, 'lockfileVersion: 9.0\nimporters:\n  .: {}\n');
+
+  assert.deepEqual(checkLockfileInstallSync(root), { status: 'out-of-sync', reason: 'stale' });
+});
+
+test('reports install-missing when a source checkout has no installed snapshot', () => {
+  const root = mkdtempForTestSync('agent-device-lockfile-sync-no-install-');
+  writeLockfile(root, 'lockfileVersion: 9.0\n');
+
+  assert.deepEqual(checkLockfileInstallSync(root), {
+    status: 'out-of-sync',
+    reason: 'install-missing',
+  });
+});
+
+test('reports install-missing for a fresh worktree that has no node_modules directory at all', () => {
+  const root = mkdtempForTestSync('agent-device-lockfile-sync-fresh-worktree-');
+  writeLockfile(root, 'lockfileVersion: 9.0\n');
+  assert.equal(fs.existsSync(path.join(root, 'node_modules')), false);
+
+  assert.deepEqual(checkLockfileInstallSync(root), {
+    status: 'out-of-sync',
+    reason: 'install-missing',
+  });
+});
+
+test('reports no-source-checkout when there is no pnpm-lock.yaml', () => {
+  const root = mkdtempForTestSync('agent-device-lockfile-sync-packaged-');
+  fs.writeFileSync(path.join(root, 'package.json'), '{"name":"agent-device"}\n');
+
+  assert.deepEqual(checkLockfileInstallSync(root), { status: 'no-source-checkout' });
+});
+
+test('reports no-source-checkout even when an installed snapshot exists without a lockfile', () => {
+  const root = mkdtempForTestSync('agent-device-lockfile-sync-no-lockfile-');
+  writeInstalledSnapshot(root, 'lockfileVersion: 9.0\n');
+
+  assert.deepEqual(checkLockfileInstallSync(root), { status: 'no-source-checkout' });
+});
+
+test('checks each worktree against its own lockfile state', () => {
+  const worktreeA = mkdtempForTestSync('agent-device-lockfile-sync-worktree-a-');
+  const worktreeB = mkdtempForTestSync('agent-device-lockfile-sync-worktree-b-');
+  writeLockfile(worktreeA, 'lockfileVersion: 9.0\nimporters:\n  .: {}\n');
+  writeInstalledSnapshot(worktreeA, 'lockfileVersion: 9.0\nimporters:\n  .: {}\n');
+  writeLockfile(
+    worktreeB,
+    'lockfileVersion: 9.0\nimporters:\n  .:\n    dependencies:\n      newDep: 1.0.0\n',
+  );
+  writeInstalledSnapshot(worktreeB, 'lockfileVersion: 9.0\nimporters:\n  .: {}\n');
+
+  assert.deepEqual(checkLockfileInstallSync(worktreeA), { status: 'in-sync' });
+  assert.deepEqual(checkLockfileInstallSync(worktreeB), { status: 'out-of-sync', reason: 'stale' });
+});
diff --git a/scripts/check-affected/lockfile-install-sync.ts b/scripts/check-affected/lockfile-install-sync.ts
new file mode 100644
index 0000000000..209ef9b4e0
--- /dev/null
+++ b/scripts/check-affected/lockfile-install-sync.ts
@@ -0,0 +1,39 @@
+import fs from 'node:fs';
+import path from 'node:path';
+
+const LOCKFILE_BASENAME = 'pnpm-lock.yaml';
+const INSTALLED_SNAPSHOT_RELATIVE_PATH = ['node_modules', '.pnpm', 'lock.yaml'];
+
+export const STALE_NODE_MODULES_MESSAGE =
+  "node_modules does not match this worktree's pnpm-lock.yaml";
+
+export type LockfileInstallSyncResult =
+  | { readonly status: 'no-source-checkout' }
+  | { readonly status: 'in-sync' }
+  | {
+      readonly status: 'out-of-sync';
+      readonly reason: 'install-missing' | 'stale';
+    };
+
+/**
+ * Compares pnpm's installed lockfile snapshot with this worktree's lockfile.
+ * This is intentionally synchronous and subprocess-free: it runs before any gate.
+ */
+export function checkLockfileInstallSync(repoRoot: string): LockfileInstallSyncResult {
+  const lockfile = readFileIfExists(path.join(repoRoot, LOCKFILE_BASENAME));
+  if (!lockfile) return { status: 'no-source-checkout' };
+
+  const installedSnapshot = readFileIfExists(
+    path.join(repoRoot, ...INSTALLED_SNAPSHOT_RELATIVE_PATH),
+  );
+  if (!installedSnapshot) return { status: 'out-of-sync', reason: 'install-missing' };
+
+  return lockfile.equals(installedSnapshot)
+    ? { status: 'in-sync' }
+    : { status: 'out-of-sync', reason: 'stale' };
+}
+
+function readFileIfExists(filePath: string): Buffer | undefined {
+  if (!fs.existsSync(filePath)) return undefined;
+  return fs.readFileSync(filePath);
+}
diff --git a/scripts/check-affected/run.test.ts b/scripts/check-affected/run.test.ts
index ac4a743eaf..58402cb696 100644
--- a/scripts/check-affected/run.test.ts
+++ b/scripts/check-affected/run.test.ts
@@ -9,6 +9,7 @@ import os from 'node:os';
 import path from 'node:path';
 import { test } from 'node:test';
 import { runCmdSync } from '../../src/utils/exec.ts';
+import { STALE_NODE_MODULES_MESSAGE } from './lockfile-install-sync.ts';
 import { CHECK_CATALOG } from './checks.ts';
 import { DEFAULT_VITEST_MAX_WORKERS } from '../lib/vitest-concurrency.ts';
 import { selectChecks } from './model.ts';
@@ -247,3 +248,111 @@ test('runChecks leaves coverage to CI and runs capped related tests once', async
     'the coverage gate is GitHub-authoritative and must not run locally',
   );
 });
+
+test('runChecks fails fast on a stale install before running format or any other check', async () => {
+  const executed: string[][] = [];
+  const execute: CommandExecutor = async (command) => {
+    executed.push(command);
+    return 0;
+  };
+  const plan = selectChecks({
+    changedFiles: ['packages/selectors/src/index.ts'],
+    packageEntryFiles: [],
+  });
+  const code = await runChecks(plan, { scripts: ALL_SCRIPTS }, ARGS, {
+    execute,
+    cwd: '.',
+    checkLockfileSync: () => ({ status: 'out-of-sync', reason: 'stale' }),
+  });
+  assert.equal(code, 1);
+  assert.deepEqual(executed, [], 'no check — including format — may run against a stale install');
+});
+
+test('runChecks fails fast when node_modules was never installed in this checkout', async () => {
+  const executed: string[][] = [];
+  const execute: CommandExecutor = async (command) => {
+    executed.push(command);
+    return 0;
+  };
+  const plan = selectChecks({
+    changedFiles: ['packages/selectors/src/index.ts'],
+    packageEntryFiles: [],
+  });
+  const code = await runChecks(plan, { scripts: ALL_SCRIPTS }, ARGS, {
+    execute,
+    cwd: '.',
+    checkLockfileSync: () => ({ status: 'out-of-sync', reason: 'install-missing' }),
+  });
+  assert.equal(code, 1);
+  assert.deepEqual(executed, []);
+});
+
+test('runChecks does not block when there is no source checkout to compare against', async () => {
+  const executed: string[][] = [];
+  const execute: CommandExecutor = async (command) => {
+    executed.push(command);
+    return 0;
+  };
+  const plan = selectChecks({
+    changedFiles: ['packages/selectors/src/index.ts'],
+    packageEntryFiles: [],
+  });
+  const code = await runChecks(plan, { scripts: ALL_SCRIPTS }, ARGS, {
+    execute,
+    cwd: '.',
+    checkLockfileSync: () => ({ status: 'no-source-checkout' }),
+  });
+  assert.equal(code, 0);
+  assert.ok(executed.length > 0, 'checks still run when there is nothing to compare against');
+});
+
+test('runChecks proceeds normally when the install is in sync', async () => {
+  const executed: string[][] = [];
+  const execute: CommandExecutor = async (command) => {
+    executed.push(command);
+    return 0;
+  };
+  const plan = selectChecks({
+    changedFiles: ['packages/selectors/src/index.ts'],
+    packageEntryFiles: [],
+  });
+  const code = await runChecks(plan, { scripts: ALL_SCRIPTS }, ARGS, {
+    execute,
+    cwd: '.',
+    checkLockfileSync: () => ({ status: 'in-sync' }),
+  });
+  assert.equal(code, 0);
+  assert.ok(executed.some((command) => command.includes('format:check')));
+});
+
+test('runChecks names the real cause on stderr instead of surfacing as an unrelated failure', async () => {
+  const stderrChunks: string[] = [];
+  const originalWrite = process.stderr.write.bind(process.stderr);
+  process.stderr.write = ((chunk: string | Uint8Array) => {
+    stderrChunks.push(chunk.toString());
+    return true;
+  }) as typeof process.stderr.write;
+
+  try {
+    const plan = selectChecks({
+      changedFiles: ['packages/selectors/src/index.ts'],
+      packageEntryFiles: [],
+    });
+    const code = await runChecks(plan, { scripts: ALL_SCRIPTS }, ARGS, {
+      execute: async () => 0,
+      cwd: '.',
+      checkLockfileSync: () => ({ status: 'out-of-sync', reason: 'stale' }),
+    });
+    assert.equal(code, 1);
+    assert.ok(
+      stderrChunks.some((chunk) => chunk.includes(STALE_NODE_MODULES_MESSAGE)),
+      `expected stderr to name the stale-install cause, got: ${stderrChunks.join('')}`,
+    );
+    const stderr = stderrChunks.join('');
+    assert.match(stderr, /Worktree: \.\n/);
+    assert.match(stderr, /pnpm install --frozen-lockfile/);
+    assert.doesNotMatch(stderr, /agent-device doctor/);
+  } finally {
+    process.stderr.write = originalWrite;
+  }
+});
diff --git a/scripts/check-affected/run.ts b/scripts/check-affected/run.ts
index d31f5bf2a9..7c4d3a2759 100644
--- a/scripts/check-affected/run.ts
+++ b/scripts/check-affected/run.ts
@@ -9,6 +9,11 @@ import fs from 'node:fs';
 import path from 'node:path';
 import { pathToFileURL } from 'node:url';
 import { runCmdStreaming, runCmdSync } from '../../src/utils/exec.ts';
+import {
+  checkLockfileInstallSync,
+  STALE_NODE_MODULES_MESSAGE,
+  type LockfileInstallSyncResult,
+} from './lockfile-install-sync.ts';
 import { parseScriptArgs } from '../lib/cli-args.ts';
 import { runEntrypoint } from '../lib/cli-entrypoint.ts';
 import {
@@ -184,9 +189,21 @@ export async function runChecks(
   plan: CheckPlan,
   pkg: PackageJson,
   args: Args,
-  options: { cwd?: string; execute?: CommandExecutor; changedFiles?: readonly string[] } = {},
+  options: {
+    cwd?: string;
+    execute?: CommandExecutor;
+    changedFiles?: readonly string[];
+    checkLockfileSync?: (cwd: string) => LockfileInstallSyncResult;
+  } = {},
 ): Promise<number> {
   const cwd = options.cwd ?? repoRoot;
+  const checkLockfileSync = options.checkLockfileSync ?? checkLockfileInstallSync;
+  // Fail before any gate can misdiagnose a stale worktree install (#1956).
+  const lockfileSync = checkLockfileSync(cwd);
+  if (lockfileSync.status === 'out-of-sync') {
+    reportStaleInstall(lockfileSync.reason, cwd);
+    return 1;
+  }
   const execute = options.execute ?? streamingExecutor;
   const runnable = plan.checks.map(getCheckSpec).filter((spec: CheckSpec) => spec.localRunnable);
   const skipped = plan.checks.map(getCheckSpec).filter((spec: CheckSpec) => !spec.localRunnable);
@@ -212,6 +229,17 @@ export async function runChecks(
   return 0;
 }
 
+function reportStaleInstall(reason: 'install-missing' | 'stale', cwd: string): void {
+  process.stderr.write(`\ncheck:affected: ${STALE_NODE_MODULES_MESSAGE}\n`);
+  process.stderr.write(
+    reason === 'install-missing'
+      ? '(no node_modules/.pnpm/lock.yaml found — this checkout was never installed)\n'
+      : '(node_modules/.pnpm/lock.yaml disagrees with pnpm-lock.yaml)\n',
+  );
+  process.stderr.write(`Worktree: ${cwd}\n`);
+  process.stderr.write('Run `pnpm install --frozen-lockfile` in this worktree, then retry.\n');
+}
+
 // Where a check the local run skips is authoritative. A parked check has no automatic
 // lane; say so instead of printing an empty job list.
 function describeOwner(id: CheckId, ciJobs: ReadonlyMap<CheckId, string[]>): string {