diff --git a/swh/indexer/metadata.py b/swh/indexer/metadata.py
--- a/swh/indexer/metadata.py
+++ b/swh/indexer/metadata.py
@@ -304,19 +304,20 @@
         revs_to_delete = []
         origs_to_delete = []
         for (orig_item, rev_item) in results:
-            assert rev_item['mappings'] == orig_item['mappings']
-            if rev_item['mappings']:
-                # Only store translated metadata if we found a metadata file.
-                # Otherwise it's just an empty dict with a "@context" key.
-                if rev_item not in rev_metadata:
-                    rev_metadata.append(rev_item)
-                if orig_item not in orig_metadata:
-                    orig_metadata.append(orig_item)
-            else:
+            assert rev_item['metadata'] == orig_item['metadata']
+            if not rev_item['metadata'] or \
+                    rev_item['metadata'].keys() <= {'@context'}:
+                # If we didn't find any metadata, don't store a DB record
+                # (and delete existing ones, if any)
                 if rev_item not in revs_to_delete:
                     revs_to_delete.append(rev_item)
                 if orig_item not in origs_to_delete:
                     origs_to_delete.append(orig_item)
+            else:
+                if rev_item not in rev_metadata:
+                    rev_metadata.append(rev_item)
+                if orig_item not in orig_metadata:
+                    orig_metadata.append(orig_item)
 
         if rev_metadata:
             self.idx_storage.revision_intrinsic_metadata_add(
@@ -326,7 +327,7 @@
                 orig_metadata, conflict_update=conflict_update)
 
         # revs_to_delete should always be empty unless we changed a mapping
-        # to detect less files.
+        # to detect less files or less content.
         # However, origs_to_delete may be empty whenever an upstream deletes
         # a metadata file.
         if origs_to_delete:
diff --git a/swh/indexer/tests/test_origin_metadata.py b/swh/indexer/tests/test_origin_metadata.py
--- a/swh/indexer/tests/test_origin_metadata.py
+++ b/swh/indexer/tests/test_origin_metadata.py
@@ -163,7 +163,7 @@
     assert len(results) == 2
 
 
-def test_origin_metadata_indexer_no_metadata(
+def test_origin_metadata_indexer_no_metadata_file(
         idx_storage, storage, obj_storage):
 
     indexer = OriginMetadataIndexer(config=REVISION_METADATA_CONFIG)
@@ -185,6 +185,52 @@
     assert results == []
 
 
+def test_origin_metadata_indexer_no_metadata(
+        idx_storage, storage, obj_storage):
+
+    indexer = OriginMetadataIndexer(config=REVISION_METADATA_CONFIG)
+    with patch('swh.indexer.metadata.RevisionMetadataIndexer'
+               '.translate_revision_intrinsic_metadata',
+               return_value=(['npm'], {'@context': 'foo'})):
+        indexer.run(["git+https://github.com/librariesio/yarn-parser"])
+
+    origin = storage.origin_get({
+        'type': 'git',
+        'url': 'https://github.com/librariesio/yarn-parser'})
+    rev_id = hash_to_bytes('8dbb6aeb036e7fd80664eb8bfd1507881af1ba9f')
+
+    results = list(
+        indexer.idx_storage.revision_intrinsic_metadata_get([rev_id]))
+    assert results == []
+
+    results = list(indexer.idx_storage.origin_intrinsic_metadata_get([
+        origin['id']]))
+    assert results == []
+
+
+def test_origin_metadata_indexer_error(
+        idx_storage, storage, obj_storage):
+
+    indexer = OriginMetadataIndexer(config=REVISION_METADATA_CONFIG)
+    with patch('swh.indexer.metadata.RevisionMetadataIndexer'
+               '.translate_revision_intrinsic_metadata',
+               return_value=None):
+        indexer.run(["git+https://github.com/librariesio/yarn-parser"])
+
+    origin = storage.origin_get({
+        'type': 'git',
+        'url': 'https://github.com/librariesio/yarn-parser'})
+    rev_id = hash_to_bytes('8dbb6aeb036e7fd80664eb8bfd1507881af1ba9f')
+
+    results = list(
+        indexer.idx_storage.revision_intrinsic_metadata_get([rev_id]))
+    assert results == []
+
+    results = list(indexer.idx_storage.origin_intrinsic_metadata_get([
+        origin['id']]))
+    assert results == []
+
+
 def test_origin_metadata_indexer_delete_metadata(
         idx_storage, storage, obj_storage):