diff --git a/swh/indexer/metadata.py b/swh/indexer/metadata.py
--- a/swh/indexer/metadata.py
+++ b/swh/indexer/metadata.py
@@ -297,13 +297,21 @@
         return (orig_metadata, rev_metadata)
 
     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)
+                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
@@ -122,3 +122,13 @@
     for result in results:
         del result['tool']
     assert results == [origin_metadata]
+
+
+@origin_metadata_indexer_test
+def test_origin_metadata_indexer_duplicates(storage, idx_storage):
+    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)