diff --git a/swh/indexer/metadata.py b/swh/indexer/metadata.py
--- a/swh/indexer/metadata.py
+++ b/swh/indexer/metadata.py
@@ -293,14 +293,37 @@
         # Deduplicate revisions
         rev_metadata = []
         orig_metadata = []
+        revs_to_delete = set()
+        origs_to_delete = set()
         for (orig_item, rev_item) in results:
-            if rev_item not in rev_metadata:
-                rev_metadata.append(rev_item)
-            if orig_item not in orig_metadata:
-                orig_metadata.append(orig_item)
-
-        self.idx_storage.revision_metadata_add(
-            rev_metadata, conflict_update=conflict_update)
-
-        self.idx_storage.origin_intrinsic_metadata_add(
-            orig_metadata, conflict_update=conflict_update)
+            assert rev_item['mappings'] == orig_item['mappings']
+            if rev_item['mappings']:
+                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:
+                revs_to_delete.add((
+                    rev_item['id'],
+                    rev_item['indexer_configuration_id'],
+                ))
+                origs_to_delete.add((
+                    orig_item['origin_id'],
+                    orig_item['indexer_configuration_id'],
+                ))
+
+        if rev_metadata:
+            self.idx_storage.revision_metadata_add(
+                rev_metadata, conflict_update=conflict_update)
+        if orig_metadata:
+            self.idx_storage.origin_intrinsic_metadata_add(
+                orig_metadata, conflict_update=conflict_update)
+
+        # revs_to_delete should always be empty unless we changed a mapping
+        # to detect less files.
+        # However, origs_to_delete may be empty whenever an upstream deletes
+        # a metadata file.
+        for (orig_id, tool_id) in origs_to_delete:
+            self.idx_storage.origin_intrinsic_metadata_delete(orig_id, tool_id)
+        for (rev_id, tool_id) in revs_to_delete:
+            self.idx_storage.revision_metadata_delete(rev_id, tool_id)
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
@@ -3,6 +3,8 @@
 # License: GNU General Public License version 3, or any later version
 # See top-level LICENSE file for more information
 
+from unittest.mock import patch
+
 from swh.model.hashutil import hash_to_bytes
 
 from swh.indexer.metadata import OriginMetadataIndexer
@@ -155,3 +157,54 @@
     results = list(indexer.idx_storage.origin_intrinsic_metadata_get([
         origin1['id'], origin2['id']]))
     assert len(results) == 2
+
+
+def test_origin_metadata_indexer_no_metadata(
+        idx_storage, storage, obj_storage):
+
+    indexer = OriginMetadataIndexer(config=REVISION_METADATA_CONFIG)
+    with patch('swh.indexer.metadata_dictionary.NpmMapping.filename',
+               b'foo.json'):
+        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_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):
+
+    indexer = OriginMetadataIndexer(config=REVISION_METADATA_CONFIG)
+    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_metadata_get([rev_id]))
+    assert results != []
+
+    results = list(indexer.idx_storage.origin_intrinsic_metadata_get([
+        origin['id']]))
+    assert results != []
+
+    with patch('swh.indexer.metadata_dictionary.NpmMapping.filename',
+               b'foo.json'):
+        indexer.run(["git+https://github.com/librariesio/yarn-parser"])
+
+    results = list(indexer.idx_storage.revision_metadata_get([rev_id]))
+    assert results == []
+
+    results = list(indexer.idx_storage.origin_intrinsic_metadata_get([
+        origin['id']]))
+    assert results == []