diff --git a/.gitignore b/.gitignore
index 75301742a..8d8f5afbc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,6 +15,7 @@
 /fixtures/build/dir010/*.phar
 /fixtures/build/dir011/*.phar
 /fixtures/build/dir011/*output
+/fixtures/build/dir011/phar-Y.php
 /fixtures/check-requirements/*/actual-output
 /fixtures/check-requirements/*/expected-output-*
 /fixtures/check-requirements/*/*.phar
diff --git a/Makefile b/Makefile
index e2fa207c0..8f607df36 100644
--- a/Makefile
+++ b/Makefile
@@ -95,9 +95,12 @@ e2e_scoper_whitelist: 	 ## Runs the end-to-end tests to check that the PHP-Scope
 e2e_scoper_whitelist: box fixtures/build/dir011/vendor
 	php fixtures/build/dir011/index.php > fixtures/build/dir011/expected-output
 	./box compile --working-dir fixtures/build/dir011
+
 	php fixtures/build/dir011/index.phar > fixtures/build/dir011/output
+	cd fixtures/build/dir011 && php -r "file_put_contents('phar-Y.php', file_get_contents((new Phar('index.phar'))['src/Y.php']));"
 
 	diff fixtures/build/dir011/expected-output fixtures/build/dir011/output
+	diff fixtures/build/dir011/phar-Y.php fixtures/build/dir011/src/Y.php
 
 .PHONY: e2e_check_requirements
 DOCKER=docker run -i --rm -w /opt/box
diff --git a/fixtures/build/dir011/scoper.inc.php b/fixtures/build/dir011/scoper.inc.php
index 719f4b21a..33b72d55f 100644
--- a/fixtures/build/dir011/scoper.inc.php
+++ b/fixtures/build/dir011/scoper.inc.php
@@ -14,4 +14,5 @@
 
 return [
     'whitelist' => ['Foo\back'],
+    'files-whitelist' => ['src/Y.php'],
 ];
diff --git a/fixtures/build/dir011/src/Y.php b/fixtures/build/dir011/src/Y.php
new file mode 100644
index 000000000..9534d0f9c
--- /dev/null
+++ b/fixtures/build/dir011/src/Y.php
@@ -0,0 +1,21 @@
+<?php
+
+declare(strict_types=1);
+
+/*
+ * This file is part of the box project.
+ *
+ * (c) Kevin Herrera <kevin@herrera.io>
+ *     Théo Fidry <theo.fidry@gmail.com>
+ *
+ * This source file is subject to the MIT license that is bundled
+ * with this source code in the file LICENSE.
+ */
+
+final class Y
+{
+    public static function salute(): void
+    {
+        echo 'World';
+    }
+}
diff --git a/scoper.inc.php b/scoper.inc.php
index ab47bbf29..5dd34748a 100644
--- a/scoper.inc.php
+++ b/scoper.inc.php
@@ -14,8 +14,6 @@
 
 use Isolated\Symfony\Component\Finder\Finder;
 
-$classLoaderContents = file_get_contents(__DIR__.'/vendor/composer/composer/src/Composer/Autoload/ClassLoader.php');
-
 return [
     'patchers' => [
         function (string $filePath, string $prefix, string $contents): string {
@@ -65,9 +63,6 @@ function (string $filePath, string $prefix, string $contents): string {
                 $contents
             );
         },
-        function (string $filePath, string $prefix, string $contents) use ($classLoaderContents): string {
-            return 'vendor/composer/composer/src/Composer/Autoload/ClassLoader.php' === $filePath ? $classLoaderContents : $contents;
-        },
         function (string $filePath, string $prefix, string $contents): string {
             if ('vendor/paragonie/sodium_compat/autoload.php' !== $filePath) {
                 return $contents;
@@ -105,6 +100,9 @@ function (string $filePath, string $prefix, string $contents): string {
             );
         },
     ],
+    'files-whitelist' => [
+        __DIR__.'/vendor/composer/composer/src/Composer/Autoload/ClassLoader.php',
+    ],
     'whitelist' => [
         \Composer\Autoload\ClassLoader::class,
 
diff --git a/src/Configuration.php b/src/Configuration.php
index bc524a0d8..37cbca25e 100644
--- a/src/Configuration.php
+++ b/src/Configuration.php
@@ -23,6 +23,7 @@
 use Humbug\PhpScoper\Configuration as PhpScoperConfiguration;
 use Humbug\PhpScoper\Console\ApplicationFactory;
 use Humbug\PhpScoper\Scoper;
+use Humbug\PhpScoper\Scoper\FileWhitelistScoper;
 use InvalidArgumentException;
 use KevinGH\Box\Compactor\Php as PhpCompactor;
 use KevinGH\Box\Compactor\PhpScoper as PhpScoperCompactor;
@@ -2444,6 +2445,21 @@ public static function createScoper(): Scoper
             }
         })::createScoper();
 
+        if ([] !== $phpScoperConfig->getWhitelistedFiles()) {
+            $whitelistedFiles = array_values(
+                array_unique(
+                    array_map(
+                        static function (string $path) use ($basePath): string {
+                            return make_path_relative($path, $basePath);
+                        },
+                        $phpScoperConfig->getWhitelistedFiles()
+                    )
+                )
+            );
+
+            $phpScoper = new FileWhitelistScoper($phpScoper, ...$whitelistedFiles);
+        }
+
         $prefix = null === $phpScoperConfig->getPrefix()
             ? unique_id('_HumbugBox')
             : $phpScoperConfig->getPrefix()