diff --git a/package_manager/src/PathExcluder/UnknownPathExcluder.php b/package_manager/src/PathExcluder/UnknownPathExcluder.php
index d0ae54dbc349e1ece78d238bc83805d84d49b0c7..163c4c40d18a971e311a80c0bda2dacc36be92f8 100644
--- a/package_manager/src/PathExcluder/UnknownPathExcluder.php
+++ b/package_manager/src/PathExcluder/UnknownPathExcluder.php
@@ -64,7 +64,8 @@ final class UnknownPathExcluder implements EventSubscriberInterface {
     // @todo Refactor in https://www.drupal.org/project/automatic_updates/issues/3334994.
     $core_packages = $event->stage->getActiveComposer()->getCorePackages();
     $scaffold_files_paths = $this->getScaffoldFiles($core_packages);
-    $paths_in_project_root = glob("$project_root/*");
+    // Search for all files (including hidden ones) in project root.
+    $paths_in_project_root = glob("$project_root/{,.}*", GLOB_BRACE);
     $paths = [];
     $known_paths = array_merge([$vendor_dir, $web_root, "$project_root/composer.json", "$project_root/composer.lock"], $scaffold_files_paths);
     foreach ($paths_in_project_root as $path_in_project_root) {
diff --git a/package_manager/tests/src/Kernel/PathExcluder/UnknownPathExcluderTest.php b/package_manager/tests/src/Kernel/PathExcluder/UnknownPathExcluderTest.php
index c56be2627045df2bf71de554e02acebc4dc22381..642047efddf0ee7d23eaf94313f463d7cbe6fedb 100644
--- a/package_manager/tests/src/Kernel/PathExcluder/UnknownPathExcluderTest.php
+++ b/package_manager/tests/src/Kernel/PathExcluder/UnknownPathExcluderTest.php
@@ -94,6 +94,16 @@ class UnknownPathExcluderTest extends PackageManagerKernelTestBase {
         NULL,
         ['unknown_file.txt'],
       ],
+      'unknown hidden file where web and project root same' => [
+        FALSE,
+        NULL,
+        ['.unknown_file'],
+      ],
+      'unknown hidden file where web and project root different' => [
+        TRUE,
+        NULL,
+        ['.unknown_file'],
+      ],
       'unknown directory where web and project root same' => [
         FALSE,
         'unknown_dir',
@@ -104,6 +114,16 @@ class UnknownPathExcluderTest extends PackageManagerKernelTestBase {
         'unknown_dir',
         ['unknown_dir/unknown_dir.README.md', 'unknown_dir/unknown_file.txt'],
       ],
+      'unknown hidden directory where web and project root same' => [
+        FALSE,
+        '.unknown_dir',
+        ['.unknown_dir/unknown_dir.README.md', '.unknown_dir/unknown_file.txt'],
+      ],
+      'unknown hidden directory where web and project root different' => [
+        TRUE,
+        '.unknown_dir',
+        ['.unknown_dir/unknown_dir.README.md', '.unknown_dir/unknown_file.txt'],
+      ],
     ];
   }