diff --git a/packages/core/core/src/RequestTracker.js b/packages/core/core/src/RequestTracker.js
index 5c9cb7169..32309f861 100644
--- a/packages/core/core/src/RequestTracker.js
+++ b/packages/core/core/src/RequestTracker.js
@@ -1510,7 +1510,7 @@ export default class RequestTracker {
       let opts = getWatcherOptions(this.options);
       let snapshotPath = path.join(this.options.cacheDir, snapshotKey + '.txt');
 
-      await this.options.inputFS.writeSnapshot(
+      await this.options.outputFS.writeSnapshot(
         this.options.watchDir,
         snapshotPath,
         opts,
diff --git a/packages/core/core/test/TargetRequest.test.js b/packages/core/core/test/TargetRequest.test.js
index b74d4ad19..2a86d7780 100644
--- a/packages/core/core/test/TargetRequest.test.js
+++ b/packages/core/core/test/TargetRequest.test.js
@@ -1243,7 +1243,7 @@ describe('TargetResolver', () => {
       [
         {
           name: 'default',
-          distDir: '.atlaspack-cache/dist',
+          distDir: serveDistDir,
           publicUrl: '/',
           env: {
             id: 'd6ea1d42532a7575',
diff --git a/packages/core/core/test/test-utils.js b/packages/core/core/test/test-utils.js
index a9e42973e..786a16a34 100644
--- a/packages/core/core/test/test-utils.js
+++ b/packages/core/core/test/test-utils.js
@@ -5,7 +5,6 @@ import type {Environment, AtlaspackOptions, Target} from '../src/types';
 import {DEFAULT_FEATURE_FLAGS} from '@atlaspack/feature-flags';
 import {FSCache} from '@atlaspack/cache';
 import tempy from 'tempy';
-import path from 'path';
 import {inputFS, outputFS} from '@atlaspack/test-utils';
 import {relativePath} from '@atlaspack/utils';
 import {NodePackageManager} from '@atlaspack/package-manager';
@@ -17,7 +16,7 @@ export let cache: FSCache = new FSCache(outputFS, cacheDir);
 cache.ensure();
 
 export const DEFAULT_OPTIONS: AtlaspackOptions = {
-  cacheDir: path.join(__dirname, '.atlaspack-cache'),
+  cacheDir,
   atlaspackVersion: '',
   watchDir: __dirname,
   watchIgnore: undefined,
diff --git a/packages/core/integration-tests/test/atlaspack-query.js b/packages/core/integration-tests/test/atlaspack-query.js
index 8e0bcb1f2..d421f522b 100644
--- a/packages/core/integration-tests/test/atlaspack-query.js
+++ b/packages/core/integration-tests/test/atlaspack-query.js
@@ -1,11 +1,17 @@
 // @flow
 import assert from 'assert';
 import path from 'path';
-import {bundle, describe, fsFixture, overlayFS} from '@atlaspack/test-utils';
+import {
+  bundle,
+  describe,
+  fsFixture,
+  overlayFS,
+  inputFS,
+} from '@atlaspack/test-utils';
 import {loadGraphs} from '../../../dev/query/src';
 
 describe.v2('atlaspack-query', () => {
-  it.skip('loadGraphs', async function () {
+  it('loadGraphs', async function () {
     let entries = 'index.js';
     let options = {
       mode: 'production',
@@ -14,6 +20,9 @@ describe.v2('atlaspack-query', () => {
       },
       shouldDisableCache: false,
       inputFS: overlayFS,
+      // We need to write to the default inputFS (NodeFS) as `loadGraphs` doesn't
+      // support custom FS's
+      outputFS: inputFS,
       cacheDir: path.join(__dirname, '.atlaspack-cache'),
     };
 
diff --git a/packages/core/integration-tests/test/cache.js b/packages/core/integration-tests/test/cache.js
index 54ff59202..deb100331 100644
--- a/packages/core/integration-tests/test/cache.js
+++ b/packages/core/integration-tests/test/cache.js
@@ -3532,7 +3532,7 @@ describe.v2('cache', function () {
       assert(!res.includes('BAR'));
     });
 
-    describe('pnp', function () {
+    describe.skip('pnp', function () {
       it('should invalidate when the .pnp.js file changes', async function () {
         let Module = require('module');
         let origPnpVersion = process.versions.pnp;