diff --git a/swh/indexer/codemeta.py b/swh/indexer/codemeta.py
--- a/swh/indexer/codemeta.py
+++ b/swh/indexer/codemeta.py
@@ -140,8 +140,19 @@
     merged_document = collections.defaultdict(list)
     for document in documents:
         for (key, values) in document.items():
-            for value in values:
-                if value not in merged_document[key]:
-                    merged_document[key].append(value)
+            if key == '@id':
+                # @id does not get expanded to a list
+                value = values
+
+                # Only one @id is allowed, move it to sameAs
+                if '@id' not in merged_document:
+                    merged_document['@id'] = value
+                elif value != merged_document['@id']:
+                    if value not in merged_document[SCHEMA_URI + 'sameAs']:
+                        merged_document[SCHEMA_URI + 'sameAs'].append(value)
+            else:
+                for value in values:
+                    if value not in merged_document[key]:
+                        merged_document[key].append(value)
 
     return compact(merged_document)
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
@@ -237,6 +237,58 @@
         }
         self.assertEqual(expected_results, results)
 
+    def test_merge_documents_ids(self):
+        # given
+        metadata_list = [{
+            '@context': 'https://doi.org/10.5063/schema/codemeta-2.0',
+            'id': 'http://example.org/test1',
+            'name': 'test_1',
+        }, {
+            '@context': 'https://doi.org/10.5063/schema/codemeta-2.0',
+            'id': 'http://example.org/test2',
+            'name': 'test_2',
+        }]
+
+        # when
+        results = merge_documents(metadata_list)
+
+        # then
+        expected_results = {
+            '@context': 'https://doi.org/10.5063/schema/codemeta-2.0',
+            'id': 'http://example.org/test1',
+            'schema:sameAs': 'http://example.org/test2',
+            "name": ['test_1', 'test_2']
+        }
+        self.assertEqual(expected_results, results)
+
+    def test_merge_documents_duplicate_ids(self):
+        # given
+        metadata_list = [{
+            '@context': 'https://doi.org/10.5063/schema/codemeta-2.0',
+            'id': 'http://example.org/test1',
+            'name': 'test_1',
+        }, {
+            '@context': 'https://doi.org/10.5063/schema/codemeta-2.0',
+            'id': 'http://example.org/test1',
+            'name': 'test_1b',
+        }, {
+            '@context': 'https://doi.org/10.5063/schema/codemeta-2.0',
+            'id': 'http://example.org/test2',
+            'name': 'test_2',
+        }]
+
+        # when
+        results = merge_documents(metadata_list)
+
+        # then
+        expected_results = {
+            '@context': 'https://doi.org/10.5063/schema/codemeta-2.0',
+            'id': 'http://example.org/test1',
+            'schema:sameAs': 'http://example.org/test2',
+            "name": ['test_1', 'test_1b', 'test_2']
+        }
+        self.assertEqual(expected_results, results)
+
     def test_index_content_metadata_npm(self):
         """
         testing NPM with package.json