diff --git a/swh/indexer/metadata_dictionary/base.py b/swh/indexer/metadata_dictionary/base.py
--- a/swh/indexer/metadata_dictionary/base.py
+++ b/swh/indexer/metadata_dictionary/base.py
@@ -250,6 +250,8 @@
 
         self.extra_translation(graph, root, content_dict)
 
+        self.sanitize(graph)
+
         # Convert from rdflib's internal graph representation to JSON
         s = graph.serialize(format="application/ld+json")
 
@@ -275,9 +277,22 @@
 
         return self.normalize_translation(translated_metadata)
 
+    def sanitize(self, graph: rdflib.Graph) -> None:
+        # Remove triples that make PyLD crash
+        for (subject, predicate, _) in graph.triples((None, None, rdflib.URIRef(""))):
+            graph.remove((subject, predicate, rdflib.URIRef("")))
+
+        # Should not happen, but we's better check as this may lead to incorrect data
+        invalid = False
+        for triple in graph.triples((rdflib.URIRef(""), None, None)):
+            invalid = True
+            logging.error("Empty triple subject URI: %r", triple)
+        if invalid:
+            raise ValueError("Empty triple subject(s)")
+
     def extra_translation(
         self, graph: rdflib.Graph, root: rdflib.term.Node, d: Dict[str, Any]
-    ):
+    ) -> None:
         """Called at the end of the translation process, and may add arbitrary triples
         to ``graph`` based on the input dictionary (passed as ``d``).
         """
diff --git a/swh/indexer/tests/metadata_dictionary/test_npm.py b/swh/indexer/tests/metadata_dictionary/test_npm.py
--- a/swh/indexer/tests/metadata_dictionary/test_npm.py
+++ b/swh/indexer/tests/metadata_dictionary/test_npm.py
@@ -294,6 +294,57 @@
     }
 
 
+def test_npm_empty_uris():
+    package_json = rb"""{
+  "version": "1.0.0",
+  "homepage": "",
+  "author": {
+    "name": "foo",
+    "url": "http://example.org"
+  }
+}"""
+    result = MAPPINGS["NpmMapping"]().translate(package_json)
+    assert result == {
+        "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
+        "type": "SoftwareSourceCode",
+        "author": [{"name": "foo", "type": "Person", "url": "http://example.org"}],
+        "version": "1.0.0",
+    }
+
+    package_json = rb"""{
+  "version": "1.0.0",
+  "homepage": "http://example.org",
+  "author": {
+    "name": "foo",
+    "url": ""
+  }
+}"""
+    result = MAPPINGS["NpmMapping"]().translate(package_json)
+    assert result == {
+        "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
+        "type": "SoftwareSourceCode",
+        "author": [{"name": "foo", "type": "Person"}],
+        "url": "http://example.org",
+        "version": "1.0.0",
+    }
+
+    package_json = rb"""{
+  "version": "1.0.0",
+  "homepage": "",
+  "author": {
+    "name": "foo",
+    "url": ""
+  }
+}"""
+    result = MAPPINGS["NpmMapping"]().translate(package_json)
+    assert result == {
+        "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
+        "type": "SoftwareSourceCode",
+        "author": [{"name": "foo", "type": "Person"}],
+        "version": "1.0.0",
+    }
+
+
 @settings(suppress_health_check=[HealthCheck.too_slow])
 @given(json_document_strategy(keys=list(MAPPINGS["NpmMapping"].mapping)))  # type: ignore
 def test_npm_adversarial(doc):