diff --git a/swh/indexer/metadata.py b/swh/indexer/metadata.py
--- a/swh/indexer/metadata.py
+++ b/swh/indexer/metadata.py
@@ -311,7 +311,7 @@
         for (orig_item, rev_item) in results:
             if rev_item not in rev_metadata:
                 rev_metadata.append(rev_item)
-            if rev_item not in orig_metadata:
+            if orig_item not in orig_metadata:
                 orig_metadata.append(orig_item)
 
         self.idx_storage.revision_metadata_add(
diff --git a/swh/indexer/storage/in_memory.py b/swh/indexer/storage/in_memory.py
--- a/swh/indexer/storage/in_memory.py
+++ b/swh/indexer/storage/in_memory.py
@@ -614,10 +614,12 @@
 
         """
 
+        items = []
         for item in metadata:
             item = item.copy()
             item['id'] = item.pop('origin_id')
-            self._origin_intrinsic_metadata.add([item], conflict_update)
+            items.append(item)
+        self._origin_intrinsic_metadata.add(items, conflict_update)
 
     def origin_intrinsic_metadata_search_fulltext(
             self, conjunction, limit=100):
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
@@ -1053,6 +1053,48 @@
         # metadata did change as the v2 was used to overwrite v1
         self.assertEqual(actual_metadata, expected_metadata_v2)
 
+    def test_origin_intrinsic_metadata_add__duplicate_twice(self):
+        # given
+        tool_id = self.tools['swh-metadata-detector']['id']
+
+        metadata = {
+            'developmentStatus': None,
+            'version': None,
+            'operatingSystem': None,
+            'description': None,
+            'keywords': None,
+            'issueTracker': None,
+            'name': None,
+            'author': None,
+            'relatedLink': None,
+            'url': None,
+            'license': None,
+            'maintainer': None,
+            'email': None,
+            'softwareRequirements': None,
+            'identifier': None,
+        }
+        metadata_rev = {
+            'id': self.revision_id_2,
+            'translated_metadata': metadata,
+            'mappings': ['mapping1'],
+            'indexer_configuration_id': tool_id,
+        }
+        metadata_origin = {
+            'origin_id': self.origin_id_1,
+            'metadata': metadata,
+            'indexer_configuration_id': tool_id,
+            'mappings': ['mapping1'],
+            'from_revision': self.revision_id_2,
+            }
+
+        # when
+        self.storage.revision_metadata_add([metadata_rev])
+
+        with self.assertRaises(ValueError):
+            self.storage.origin_intrinsic_metadata_add([
+                metadata_origin, metadata_origin])
+
     def test_origin_intrinsic_metadata_search_fulltext(self):
         # given
         tool_id = self.tools['swh-metadata-detector']['id']