diff --git a/swh/indexer/sql/40-swh-func.sql b/swh/indexer/sql/40-swh-func.sql
--- a/swh/indexer/sql/40-swh-func.sql
+++ b/swh/indexer/sql/40-swh-func.sql
@@ -420,7 +420,10 @@
             on conflict(id, indexer_configuration_id)
                 do update set
                     metadata = excluded.metadata,
-                    mappings = excluded.mappings;
+                    metadata_tsvector = excluded.metadata_tsvector,
+                    mappings = excluded.mappings,
+                    origin_url = excluded.origin_url,
+                    from_revision = excluded.from_revision;
 
     else
         insert into origin_intrinsic_metadata (id, origin_url, metadata, indexer_configuration_id, from_revision, metadata_tsvector, mappings)
diff --git a/swh/indexer/tests/storage/test_storage.py b/swh/indexer/tests/storage/test_storage.py
--- a/swh/indexer/tests/storage/test_storage.py
+++ b/swh/indexer/tests/storage/test_storage.py
@@ -1197,7 +1197,14 @@
         metadata_rev_v2 = metadata_rev_v1.copy()
         metadata_origin_v2 = metadata_origin_v1.copy()
         metadata_rev_v2['metadata'] = metadata_v2
-        metadata_origin_v2['metadata'] = metadata_v2
+        metadata_origin_v2 = {
+            'id': self.origin_id_1,
+            'origin_url': 'file:///dev/null',
+            'metadata': metadata_v2.copy(),
+            'indexer_configuration_id': tool_id,
+            'mappings': ['npm'],
+            'from_revision': self.revision_id_1,
+        }
 
         self.storage.revision_intrinsic_metadata_add(
                 [metadata_rev_v2], conflict_update=True)
@@ -1209,11 +1216,11 @@
 
         expected_metadata_v2 = [{
             'id': self.origin_id_1,
-            'origin_url': 'file:///dev/zero',
+            'origin_url': 'file:///dev/null',
             'metadata': metadata_v2,
             'tool': self.tools['swh-metadata-detector'],
-            'from_revision': self.revision_id_2,
-            'mappings': [],
+            'from_revision': self.revision_id_1,
+            'mappings': ['npm'],
         }]
 
         # metadata did change as the v2 was used to overwrite v1