diff --git a/swh/indexer/metadata.py b/swh/indexer/metadata.py
--- a/swh/indexer/metadata.py
+++ b/swh/indexer/metadata.py
@@ -303,13 +303,22 @@
         return results
 
     def persist_index_computations(self, results, policy_update):
+        conflict_update = (policy_update == 'update-dups')
+
+        # Deduplicate revisions
+        rev_metadata = []
+        orig_metadata = []
+        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:
+                orig_metadata.append(orig_item)
+
         self.idx_storage.revision_metadata_add(
-            [rev_item for (orig_item, rev_item) in results],
-            conflict_update=(policy_update == 'update-dups'))
+            rev_metadata, conflict_update=conflict_update)
 
         self.idx_storage.origin_intrinsic_metadata_add(
-            [orig_item for (orig_item, rev_item) in results],
-            conflict_update=(policy_update == 'update-dups'))
+            orig_metadata, conflict_update=conflict_update)
 
 
 @click.command()
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
@@ -75,3 +75,25 @@
     for result in results:
         del result['tool']
     assert results == [origin_metadata]
+
+
+def test_origin_metadata_indexer_duplicates(
+        idx_storage, storage, obj_storage, origin_metadata_indexer):
+    indexer = OriginMetadataIndexer()
+    indexer.storage = storage
+    indexer.idx_storage = idx_storage
+    indexer.run(["git+https://github.com/librariesio/yarn-parser"])
+
+    indexer.run(["git+https://github.com/librariesio/yarn-parser"]*2)
+
+    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 len(results) == 1
+
+    results = list(indexer.idx_storage.origin_intrinsic_metadata_get([
+        origin['id']]))
+    assert len(results) == 1