diff --git a/pillar/api/eve_settings.py b/pillar/api/eve_settings.py
index a475856a..b7c54cf6 100644
--- a/pillar/api/eve_settings.py
+++ b/pillar/api/eve_settings.py
@@ -720,11 +720,12 @@ tokens = {
 }
 
 files = {
+    'schema': files_schema,
     'resource_methods': ['GET', 'POST'],
     'item_methods': ['GET', 'PATCH'],
     'public_methods': ['GET'],
     'public_item_methods': ['GET'],
-    'schema': files_schema
+    'soft_delete': True,
 }
 
 groups = {
diff --git a/pillar/cli/maintenance.py b/pillar/cli/maintenance.py
index 32edec24..dc4671a5 100644
--- a/pillar/cli/maintenance.py
+++ b/pillar/cli/maintenance.py
@@ -544,7 +544,8 @@ def _find_orphan_files(project_id: bson.ObjectId) -> typing.Set[bson.ObjectId]:
 
     # Get all file IDs that belong to this project.
     files_coll = current_app.db('files')
-    cursor = files_coll.find({'project': project_id}, projection={'_id': 1})
+    file_filter = {'project': project_id, '_deleted': {'$ne': True}}
+    cursor = files_coll.find(file_filter, projection={'_id': 1})
     file_ids = {doc['_id'] for doc in cursor}
     if not file_ids:
         log.debug('Project %s has no files', project_id)