diff --git a/pungi/phases/extra_isos.py b/pungi/phases/extra_isos.py
index 98883c5d..8f42bcd7 100644
--- a/pungi/phases/extra_isos.py
+++ b/pungi/phases/extra_isos.py
@@ -342,23 +342,24 @@ def get_extra_files(compose, variant, arch, extra_files):
     included in the ISO.
     """
     extra_files_dir = compose.paths.work.extra_iso_extra_files_dir(arch, variant)
-    filelist = []
     for scm_dict in extra_files:
         getter = get_file_from_scm if "file" in scm_dict else get_dir_from_scm
         target = scm_dict.get("target", "").lstrip("/")
         target_path = os.path.join(extra_files_dir, target).rstrip("/")
-        filelist.extend(
-            os.path.join(target, f)
-            for f in getter(scm_dict, target_path, compose=compose, arch=arch)
-        )
+        getter(scm_dict, target_path, compose=compose, arch=arch)
 
+    filelist = [
+        os.path.relpath(os.path.join(root, f), extra_files_dir)
+        for root, _, files in os.walk(extra_files_dir)
+        for f in files
+    ]
     if filelist:
         metadata.populate_extra_files_metadata(
             ExtraFiles(),
             variant,
             arch,
             extra_files_dir,
-            filelist,
+            sorted(filelist),
             compose.conf["media_checksums"],
         )
 
diff --git a/tests/test_extra_isos_phase.py b/tests/test_extra_isos_phase.py
index edffde77..e80bd3b8 100644
--- a/tests/test_extra_isos_phase.py
+++ b/tests/test_extra_isos_phase.py
@@ -525,7 +525,11 @@ class GetExtraFilesTest(helpers.PungiTestCase):
         self.assertEqual(populate_md.call_args_list, [])
 
     def test_get_file(self, get_dir, get_file, populate_md):
-        get_file.return_value = ["GPL"]
+        def mock_get_file(scm_dict, target_path, compose, arch):
+            helpers.touch(os.path.join(target_path, scm_dict["file"]))
+            return [scm_dict["file"]]
+
+        get_file.side_effect = mock_get_file
         cfg = {
             "scm": "git",
             "repo": "https://pagure.io/pungi.git",
@@ -561,7 +565,13 @@ class GetExtraFilesTest(helpers.PungiTestCase):
         )
 
     def test_get_dir(self, get_dir, get_file, populate_md):
-        get_dir.return_value = ["a", "b"]
+        def mock_get_dir(scm_dict, target_path, compose, arch):
+            files = ["a", "b"]
+            for f in files:
+                helpers.touch(os.path.join(target_path, f))
+            return files
+
+        get_dir.side_effect = mock_get_dir
         cfg = {
             "scm": "git",
             "repo": "https://pagure.io/pungi.git",
@@ -597,7 +607,11 @@ class GetExtraFilesTest(helpers.PungiTestCase):
         )
 
     def test_get_multiple_files(self, get_dir, get_file, populate_md):
-        get_file.side_effect = [["GPL"], ["setup.py"]]
+        def mock_get_file(scm_dict, target_path, compose, arch):
+            helpers.touch(os.path.join(target_path, scm_dict["file"]))
+            return [scm_dict["file"]]
+
+        get_file.side_effect = mock_get_file
         cfg1 = {
             "scm": "git",
             "repo": "https://pagure.io/pungi.git",