diff --git a/.github/scripts/sync-master-to-3x.mjs b/.github/scripts/sync-master-to-3x.mjs
index d141d6358b8..2c2d30ccc0e 100644
--- a/.github/scripts/sync-master-to-3x.mjs
+++ b/.github/scripts/sync-master-to-3x.mjs
@@ -64,6 +64,9 @@
  */
 
 import { execFileSync } from 'node:child_process';
+import { randomUUID } from 'node:crypto';
+import { tmpdir } from 'node:os';
+import { join } from 'node:path';
 
 import {
 	attempt,
@@ -139,6 +142,20 @@ export function blocksLockfileRegen(codePaths) {
 	);
 }
 
+/** Run the trusted frozen install without using a store restored by the sync job. */
+export function validateLockfile(pnpm, env = process.env) {
+	const validationDir = join(env.RUNNER_TEMP || tmpdir(), `n8n-sync-lockfile-${randomUUID()}`);
+	pnpm([
+		'install',
+		'--frozen-lockfile',
+		'--trust-lockfile',
+		'--store-dir',
+		join(validationDir, 'store'),
+		'--virtual-store-dir',
+		join(validationDir, 'virtual-store'),
+	]);
+}
+
 /**
  * Resolve one mechanical path in the working tree (valid mid-merge and mid-rebase alike)
  * and stage the result.
@@ -151,8 +168,7 @@ export function resolveMechanicalPath({ git, pnpm, path, masterSha, log = consol
 		log(`Regenerating ${path} with pnpm...`);
 		pnpm(['install', '--lockfile-only', '--no-frozen-lockfile']);
 		try {
-			// Use the exact CI install command so this guard has the same behavior as CI.
-			pnpm(['install', '--frozen-lockfile', '--trust-lockfile']);
+			validateLockfile(pnpm);
 		} catch (error) {
 			git(['checkout', '--conflict=merge', '--', path]);
 			throw error;
@@ -312,8 +328,7 @@ export function reconcileWithMergeTreeAtTip({
  */
 export function reconcileLockfileAtTip({ git, pnpm, masterSha, log = console.log }) {
 	pnpm(['install', '--lockfile-only', '--no-frozen-lockfile']);
-	// Use the exact CI install command so this guard has the same behavior as CI.
-	pnpm(['install', '--frozen-lockfile', '--trust-lockfile']);
+	validateLockfile(pnpm);
 	if (attempt(git, ['diff', '--quiet', '--', LOCKFILE]).ok) return;
 	if (git(['rev-parse', 'HEAD']) === masterSha) {
 		throw new Error('Lockfile reconciliation would amend a master commit; refusing.');
diff --git a/.github/scripts/sync-master-to-3x.test.mjs b/.github/scripts/sync-master-to-3x.test.mjs
index a9dee7bfa4f..b9ffc1b9eac 100644
--- a/.github/scripts/sync-master-to-3x.test.mjs
+++ b/.github/scripts/sync-master-to-3x.test.mjs
@@ -1,4 +1,5 @@
 import assert from 'node:assert/strict';
+import { tmpdir } from 'node:os';
 import { test } from 'node:test';
 
 import {
@@ -6,6 +7,7 @@ import {
 	mergeTree,
 	classifyPaths,
 	blocksLockfileRegen,
+	validateLockfile,
 	resolveMechanicalPath,
 	resolveQueueSidePath,
 	deleteModifyConflicts,
@@ -87,6 +89,22 @@ const baseGitRoutes = [
 const env = { GH_TOKEN: 'tok', GITHUB_REPOSITORY: 'n8n-io/n8n' };
 const noOpenPr = [[(a) => a[0] === 'pr' && a[1] === 'list', '[]']];
 
+function isolatedValidationPaths(args) {
+	assert.deepEqual(args.slice(0, 3), ['install', '--frozen-lockfile', '--trust-lockfile']);
+	assert.equal(args.includes('--force'), false);
+	assert.equal(args.length, 7);
+	const storeDirIndex = args.indexOf('--store-dir');
+	const virtualStoreDirIndex = args.indexOf('--virtual-store-dir');
+	assert.ok(storeDirIndex >= 3);
+	assert.ok(virtualStoreDirIndex >= 3);
+	const storeDir = args[storeDirIndex + 1];
+	const virtualStoreDir = args[virtualStoreDirIndex + 1];
+	assert.ok(storeDir);
+	assert.ok(virtualStoreDir);
+	assert.notEqual(storeDir, virtualStoreDir);
+	return { storeDir, virtualStoreDir };
+}
+
 test('targetBranch defaults to 3.x and honours the rehearsal override', () => {
 	assert.equal(targetBranch({}), TARGET_BRANCH);
 	assert.equal(targetBranch({ SYNC_TARGET_BRANCH: '3x-sync-test' }), '3x-sync-test');
@@ -155,6 +173,23 @@ test('classifyPaths and blocksLockfileRegen split mechanical from code conflicts
 	assert.equal(blocksLockfileRegen(['packages/cli/x.ts']), false);
 });
 
+test('validateLockfile uses fresh stores under the configured temporary directory', () => {
+	const pnpm = makeStub();
+	validateLockfile(pnpm, { RUNNER_TEMP: '/runner-temp' });
+	validateLockfile(pnpm, { RUNNER_TEMP: '/runner-temp' });
+	validateLockfile(pnpm, {});
+
+	const first = isolatedValidationPaths(pnpm.calls[0]);
+	const second = isolatedValidationPaths(pnpm.calls[1]);
+	const fallback = isolatedValidationPaths(pnpm.calls[2]);
+	assert.ok(first.storeDir.startsWith('/runner-temp/'));
+	assert.ok(first.virtualStoreDir.startsWith('/runner-temp/'));
+	assert.notEqual(first.storeDir, second.storeDir);
+	assert.notEqual(first.virtualStoreDir, second.virtualStoreDir);
+	assert.ok(fallback.storeDir.startsWith(`${tmpdir()}/`));
+	assert.ok(fallback.virtualStoreDir.startsWith(`${tmpdir()}/`));
+});
+
 test('resolveMechanicalPath takes the blob from master, or the deletion when master removed the file', () => {
 	const present = makeStub([[(a) => a[0] === 'cat-file', '']]);
 	resolveMechanicalPath({
@@ -185,11 +220,10 @@ test('resolveMechanicalPath regenerates and applies patches before staging the l
 	const git = makeStub();
 	const pnpm = makeStub();
 	resolveMechanicalPath({ git, pnpm, path: LOCKFILE, masterSha: MASTER, log: () => {} });
-	// Regeneration must override CI's frozen default. Validation must use the exact CI command.
-	assert.deepEqual(pnpm.calls, [
-		['install', '--lockfile-only', '--no-frozen-lockfile'],
-		['install', '--frozen-lockfile', '--trust-lockfile'],
-	]);
+	// Regeneration must override CI's frozen default. Validation must use isolated stores.
+	assert.deepEqual(pnpm.calls[0], ['install', '--lockfile-only', '--no-frozen-lockfile']);
+	isolatedValidationPaths(pnpm.calls[1]);
+	assert.equal(pnpm.calls.length, 2);
 	assert.ok(git.calls.some((a) => a[0] === 'add' && a.includes(LOCKFILE)));
 });
 
@@ -419,10 +453,9 @@ test('reconcileLockfileAtTip folds an inconsistent lockfile into the tip commit,
 	]);
 	const pnpm = makeStub();
 	reconcileLockfileAtTip({ git: inconsistent, pnpm, masterSha: MASTER, log: () => {} });
-	assert.deepEqual(pnpm.calls, [
-		['install', '--lockfile-only', '--no-frozen-lockfile'],
-		['install', '--frozen-lockfile', '--trust-lockfile'],
-	]);
+	assert.deepEqual(pnpm.calls[0], ['install', '--lockfile-only', '--no-frozen-lockfile']);
+	isolatedValidationPaths(pnpm.calls[1]);
+	assert.equal(pnpm.calls.length, 2);
 	assert.ok(inconsistent.calls.some((a) => a[0] === 'commit' && a.includes('--amend')));
 
 	const validationGit = makeStub();
@@ -686,17 +719,11 @@ test('sync auto-resolves a lockfile-only conflict during the replay — no PR, n
 
 	// The stall regen and tip reconciliation each run regeneration and exact CI validation.
 	assert.deepEqual(pnpm.calls[0], ['install', '--lockfile-only', '--no-frozen-lockfile']);
-	assert.deepEqual(pnpm.calls[1], [
-		'install',
-		'--frozen-lockfile',
-		'--trust-lockfile',
-	]);
+	const stallValidation = isolatedValidationPaths(pnpm.calls[1]);
 	assert.deepEqual(pnpm.calls[2], ['install', '--lockfile-only', '--no-frozen-lockfile']);
-	assert.deepEqual(pnpm.calls[3], [
-		'install',
-		'--frozen-lockfile',
-		'--trust-lockfile',
-	]);
+	const tipValidation = isolatedValidationPaths(pnpm.calls[3]);
+	assert.notEqual(stallValidation.storeDir, tipValidation.storeDir);
+	assert.notEqual(stallValidation.virtualStoreDir, tipValidation.virtualStoreDir);
 	assert.equal(pnpm.calls.length, 4);
 	assert.ok(git.calls.some((a) => a[0] === 'add' && a.includes(LOCKFILE)));
 	assert.ok(git.calls.some((a) => a[0] === 'rebase' && a[1] === '--continue'));
@@ -844,10 +871,9 @@ test('buildConflictBranch pre-resolves mechanical files so only code conflicts r
 	assert.deepEqual(files, ['packages/cli/x.ts']);
 	assert.deepEqual(preResolved, [LOCKFILE, POPULARITY]);
 	assert.equal(lockfileDeferred, false);
-	assert.deepEqual(pnpm.calls, [
-		['install', '--lockfile-only', '--no-frozen-lockfile'],
-		['install', '--frozen-lockfile', '--trust-lockfile'],
-	]);
+	assert.deepEqual(pnpm.calls[0], ['install', '--lockfile-only', '--no-frozen-lockfile']);
+	isolatedValidationPaths(pnpm.calls[1]);
+	assert.equal(pnpm.calls.length, 2);
 	assert.ok(
 		git.calls.some((a) => a[0] === 'checkout' && a[1] === MASTER && a.includes(POPULARITY)),
 	);
@@ -892,10 +918,9 @@ test('buildConflictBranch restores and defers a lockfile when the patched instal
 	assert.deepEqual(files, ['packages/cli/x.ts']);
 	assert.deepEqual(preResolved, []);
 	assert.equal(lockfileDeferred, true);
-	assert.deepEqual(pnpm.calls, [
-		['install', '--lockfile-only', '--no-frozen-lockfile'],
-		['install', '--frozen-lockfile', '--trust-lockfile'],
-	]);
+	assert.deepEqual(pnpm.calls[0], ['install', '--lockfile-only', '--no-frozen-lockfile']);
+	isolatedValidationPaths(pnpm.calls[1]);
+	assert.equal(pnpm.calls.length, 2);
 	assert.ok(
 		git.calls.some(
 			(a) =>