diff --git a/.changeset/silent-ears-wonder.md b/.changeset/silent-ears-wonder.md
new file mode 100644
index 0000000000..6aee510813
--- /dev/null
+++ b/.changeset/silent-ears-wonder.md
@@ -0,0 +1,6 @@
+---
+'@atlaspack/feature-flags': patch
+'@atlaspack/core': patch
+---
+
+Clean-up patch project paths feature-flag
diff --git a/packages/core/core/src/projectPath.js b/packages/core/core/src/projectPath.js
index cc3e701786..eb8a168c9b 100644
--- a/packages/core/core/src/projectPath.js
+++ b/packages/core/core/src/projectPath.js
@@ -1,8 +1,7 @@
 // @flow strict-local
 import type {FilePath} from '@atlaspack/types';
 import path from 'path';
-import {relativePath, normalizeSeparators} from '@atlaspack/utils';
-import {getFeatureFlagValue} from '@atlaspack/feature-flags';
+import {relativePath} from '@atlaspack/utils';
 
 /**
  * A path that's relative to the project root.
@@ -30,19 +29,9 @@ function toProjectPath_(projectRoot: FilePath, p: FilePath): ProjectPath {
     return p;
   }
 
-  // If the file is outside the project root, store an absolute path rather than a relative one.
-  // This way if the project root is moved, the file references still work. Accessing files outside
-  // the project root is not portable anyway.
+  // If the file is outside the project root, we store a relative path.
+  // Relative paths make the cache portable across machines.
   let relative = relativePath(projectRoot, p, false);
-  if (relative.startsWith('..')) {
-    // e.g given projectRoot = '/Users/monorepo/project' and p = '/Users/monorepo/other-project/src/index.js' --> relative = '../other-project/src/index.js'
-    if (getFeatureFlagValue('patchProjectPaths')) {
-      return relative;
-    }
-
-    return process.platform === 'win32' ? normalizeSeparators(p) : p;
-  }
-
   return relative;
 }
 
diff --git a/packages/core/core/test/TargetRequest.test.js b/packages/core/core/test/TargetRequest.test.js
index 8881fe8092..2b9f6cfb8f 100644
--- a/packages/core/core/test/TargetRequest.test.js
+++ b/packages/core/core/test/TargetRequest.test.js
@@ -5,7 +5,7 @@ import path from 'path';
 import tempy from 'tempy';
 import {inputFS as fs} from '@atlaspack/test-utils';
 import {md} from '@atlaspack/diagnostic';
-import {normalizeSeparators} from '@atlaspack/utils';
+import {relativePath} from '@atlaspack/utils';
 import {TargetResolver} from '../src/requests/TargetRequest';
 import {DEFAULT_OPTIONS as _DEFAULT_OPTIONS, relative} from './test-utils';
 
@@ -123,7 +123,10 @@ describe('TargetResolver', () => {
         {
           name: 'customA',
           publicUrl: '/',
-          distDir: normalizeSeparators(path.resolve('customA')),
+          distDir: relativePath(
+            DEFAULT_OPTIONS.projectRoot,
+            path.resolve('customA'),
+          ),
           env: {
             id: 'd821e85f6b50315e',
             context: 'browser',
@@ -145,7 +148,10 @@ describe('TargetResolver', () => {
           name: 'customB',
           publicUrl: '/',
           distEntry: 'b.js',
-          distDir: normalizeSeparators(path.resolve('customB')),
+          distDir: relativePath(
+            DEFAULT_OPTIONS.projectRoot,
+            path.resolve('customB'),
+          ),
           env: {
             id: 'e45cc12216f7857d',
             context: 'node',
@@ -631,7 +637,10 @@ describe('TargetResolver', () => {
       [
         {
           name: 'customB',
-          distDir: normalizeSeparators(path.resolve('customB')),
+          distDir: relativePath(
+            DEFAULT_OPTIONS.projectRoot,
+            path.resolve('customB'),
+          ),
           publicUrl: '/',
           env: {
             id: 'd821e85f6b50315e',
@@ -674,7 +683,10 @@ describe('TargetResolver', () => {
       [
         {
           name: 'customA',
-          distDir: normalizeSeparators(path.resolve('customA')),
+          distDir: relativePath(
+            DEFAULT_OPTIONS.projectRoot,
+            path.resolve('customA'),
+          ),
           publicUrl: '/',
           env: {
             id: 'd821e85f6b50315e',
@@ -1263,7 +1275,7 @@ describe('TargetResolver', () => {
       [
         {
           name: 'default',
-          distDir: serveDistDir,
+          distDir: relativePath(DEFAULT_OPTIONS.projectRoot, serveDistDir),
           publicUrl: '/',
           env: {
             id: '858b9b5a5dca37d4',
diff --git a/packages/core/feature-flags/src/index.js b/packages/core/feature-flags/src/index.js
index f8a2bf3ce8..c2634a99ed 100644
--- a/packages/core/feature-flags/src/index.js
+++ b/packages/core/feature-flags/src/index.js
@@ -26,7 +26,6 @@ export const DEFAULT_FEATURE_FLAGS: FeatureFlags = {
   reduceResolverStringCreation: false,
   inlineBundlesSourceMapFixes: false,
   conditionalBundlingNestedRuntime: false,
-  patchProjectPaths: false,
   cachePerformanceImprovements: process.env.NODE_ENV === 'test',
   environmentDeduplication: false,
   inlineStringReplacementPerf: false,
diff --git a/packages/core/feature-flags/src/types.js b/packages/core/feature-flags/src/types.js
index 38215dd50b..e9d5e05527 100644
--- a/packages/core/feature-flags/src/types.js
+++ b/packages/core/feature-flags/src/types.js
@@ -73,10 +73,6 @@ export type FeatureFlags = {|
    * Enable nested loading of bundles in the runtime with conditional bundling
    */
   conditionalBundlingNestedRuntime: boolean,
-  /** Enable patch project paths. This will patch the project paths to be relative to the project root.
-   * This feature is experimental and should not be used in production. It will used to test downloadble cache artefacts.
-   */
-  patchProjectPaths: boolean,
   /**
    * Enables optimized inline string replacement perf for the packager.
    * Used heavily for inline bundles.
diff --git a/packages/core/test-utils/src/utils.js b/packages/core/test-utils/src/utils.js
index 433beeb731..6388dbc5b4 100644
--- a/packages/core/test-utils/src/utils.js
+++ b/packages/core/test-utils/src/utils.js
@@ -502,9 +502,17 @@ export async function runBundle(
         if (src.hostname == null) {
           let p = path.join(distDir, nullthrows(src.pathname));
           let b = nullthrows(
-            bundles.find(
-              (b) => b.bundleBehavior !== 'inline' && b.filePath === p,
-            ),
+            bundles.find((b) => {
+              // This is not right.
+              // What is happening is that the bundle distDir is set to a relative path as of `patchProjectPaths`
+              // However, the bundle filePath is still set to an absolute path, just a non-resolved one.
+              //
+              // We should make sure that the bundle file-paths stored are also stored as relative to the project root
+              // not as absolute paths.
+              return (
+                b.bundleBehavior !== 'inline' && path.resolve(b.filePath) === p
+              );
+            }),
           );
           scripts.push([overlayFS.readFileSync(b.filePath, 'utf8'), b]);
         }