diff --git a/invenio_utilities_tuw/cli/files.py b/invenio_utilities_tuw/cli/files.py
index 95d8790f7596894b7d6a0aa410a1d7d70b897b2a..326e1d0c7a152c9f8761f364ab89d86167a88e94 100644
--- a/invenio_utilities_tuw/cli/files.py
+++ b/invenio_utilities_tuw/cli/files.py
@@ -49,7 +49,10 @@ def get_orphaned_files(location):
     # filter out those files that invenio has knowledge about
     for bucket in location.buckets:
         for obj in bucket.objects:
-            all_files.remove(obj.file.uri)
+            if obj.file:
+                # an object_version without attached file_instance
+                # likely denotes a soft-deleted file
+                all_files.remove(obj.file.uri)
 
     return all_files