diff --git a/swh/indexer/metadata.py b/swh/indexer/metadata.py
--- a/swh/indexer/metadata.py
+++ b/swh/indexer/metadata.py
@@ -5,7 +5,6 @@
 
 from copy import deepcopy
 import hashlib
-import itertools
 import logging
 import time
 from typing import (
@@ -84,14 +83,15 @@
             for item in objects.get("raw_extrinsic_metadata", []):
                 remd = RawExtrinsicMetadata.from_dict(item)
                 sentry_sdk.set_tag("swh-indexer-remd-swhid", str(remd.swhid()))
-                results[remd.target] = self.index(remd.id, data=remd)
+                for result in self.index(remd.id, data=remd):
+                    results[result.id] = result
         except Exception:
             if not self.catch_exceptions:
                 raise
             summary["status"] = "failed"
             return summary
 
-        self.results = list(itertools.chain.from_iterable(results.values()))
+        self.results = list(results.values())
         summary_persist = self.persist_index_computations(self.results)
         if summary_persist:
             for value in summary_persist.values():
diff --git a/swh/indexer/tests/test_metadata.py b/swh/indexer/tests/test_metadata.py
--- a/swh/indexer/tests/test_metadata.py
+++ b/swh/indexer/tests/test_metadata.py
@@ -390,7 +390,7 @@
         assert results == []
 
     def test_extrinsic_metadata_indexer_duplicate_origin(self, mocker):
-        """Nominal case, calling the mapping and storing the result"""
+        """Two metadata objects with the same origin target"""
         origin = "https://example.org/jdoe/myrepo"
 
         metadata_indexer = ExtrinsicMetadataIndexer(config=DIRECTORY_METADATA_CONFIG)
@@ -417,3 +417,36 @@
         )
         assert len(results) == 1, results
         assert results[0].from_remd_id == b"\x00" * 20
+
+    def test_extrinsic_directory_metadata_indexer_duplicate_origin(self, mocker):
+        """Two metadata objects on directories, but with an origin context"""
+        origin = DEPOSIT_REMD.origin
+
+        metadata_indexer = ExtrinsicMetadataIndexer(config=DIRECTORY_METADATA_CONFIG)
+        metadata_indexer.catch_exceptions = False
+        metadata_indexer.storage = mocker.patch.object(metadata_indexer, "storage")
+        metadata_indexer.storage.origin_get_by_sha1.return_value = [{"url": origin}]
+
+        tool = metadata_indexer.idx_storage.indexer_configuration_get(
+            {f"tool_{k}": v for (k, v) in TRANSLATOR_TOOL.items()}
+        )
+        assert tool is not None
+
+        assert metadata_indexer.process_journal_objects(
+            {
+                "raw_extrinsic_metadata": [
+                    DEPOSIT_REMD.to_dict(),
+                    {
+                        **DEPOSIT_REMD.to_dict(),
+                        "id": b"\x00" * 20,
+                        "target": "swh:1:dir:" + "01" * 20,
+                    },
+                ]
+            }
+        ) == {"status": "eventful", "origin_extrinsic_metadata:add": 1}
+
+        results = list(
+            metadata_indexer.idx_storage.origin_extrinsic_metadata_get([origin])
+        )
+        assert len(results) == 1, results
+        assert results[0].from_remd_id == b"\x00" * 20