diff --git a/scripts/post_deploy_tdr.py b/scripts/post_deploy_tdr.py
index 98c680f31..40411592f 100644
--- a/scripts/post_deploy_tdr.py
+++ b/scripts/post_deploy_tdr.py
@@ -102,7 +102,7 @@ def verify_source(self,
             require(prefix.common == '', source_spec)
             self.tdr.check_bigquery_access(source_spec)
         else:
-            subgraph_count = len(plugin.list_bundles(ref, prefix.common))
+            subgraph_count = plugin.count_bundles(ref.spec)
             require(subgraph_count > 0, 'Common prefix is too long', ref.spec)
             require(subgraph_count <= 512, 'Common prefix is too short', ref.spec)
 
diff --git a/src/azul/plugins/__init__.py b/src/azul/plugins/__init__.py
index 893499fb2..c7dffb65e 100644
--- a/src/azul/plugins/__init__.py
+++ b/src/azul/plugins/__init__.py
@@ -615,9 +615,10 @@ def _lookup_source_id(self, spec: SOURCE_SPEC) -> str:
         raise NotImplementedError
 
     @abstractmethod
-    def _count_subgraphs(self, source: SOURCE_SPEC) -> int:
+    def count_bundles(self, source: SOURCE_SPEC) -> int:
         """
-        The total number of subgraphs in the given source, ignoring its prefix.
+        The total number of subgraphs in the given source. The source's prefix
+        may be None.
         """
         raise NotImplementedError
 
@@ -631,7 +632,7 @@ def partition_source(self,
         should be appropriate for indexing in the given catalog.
         """
         if source.spec.prefix is None:
-            count = self._count_subgraphs(source.spec)
+            count = self.count_bundles(source.spec)
             is_main = config.deployment.is_main
             is_it = catalog in config.integration_test_catalogs
             # We use the "lesser" heuristic during IT to avoid indexing an
diff --git a/src/azul/plugins/repository/canned/__init__.py b/src/azul/plugins/repository/canned/__init__.py
index 3c2705fdf..ea4c35f9e 100644
--- a/src/azul/plugins/repository/canned/__init__.py
+++ b/src/azul/plugins/repository/canned/__init__.py
@@ -26,6 +26,9 @@
 from furl import (
     furl,
 )
+from more_itertools import (
+    ilen,
+)
 
 from azul import (
     CatalogName,
@@ -163,9 +166,13 @@ def staging_area(self, url: str) -> StagingArea:
                                                             ref)
             return factory.load_staging_area(path)
 
-    def _count_subgraphs(self, source: SOURCE_SPEC) -> int:
+    def count_bundles(self, source: SOURCE_SPEC) -> int:
         staging_area = self.staging_area(source.spec.name)
-        return len(staging_area.links)
+        return ilen(
+            links_id
+            for links_id in staging_area.links
+            if source.prefix is None or links_id.startswith(source.prefix.common)
+        )
 
     def list_bundles(self,
                      source: CannedSourceRef,
diff --git a/src/azul/plugins/repository/dss/__init__.py b/src/azul/plugins/repository/dss/__init__.py
index 96a6da973..4e5809f4a 100644
--- a/src/azul/plugins/repository/dss/__init__.py
+++ b/src/azul/plugins/repository/dss/__init__.py
@@ -118,7 +118,7 @@ def sources(self) -> AbstractSet[SimpleSourceSpec]:
     def _lookup_source_id(self, spec: SimpleSourceSpec) -> str:
         return DSSSourceRef.id_from_spec(spec)
 
-    def _count_subgraphs(self, source: SimpleSourceSpec) -> NoReturn:
+    def count_bundles(self, source: SimpleSourceSpec) -> NoReturn:
         assert False, 'DSS is EOL'
 
     def list_sources(self,
diff --git a/src/azul/plugins/repository/tdr_anvil/__init__.py b/src/azul/plugins/repository/tdr_anvil/__init__.py
index 3d7afc2b9..13449cd52 100644
--- a/src/azul/plugins/repository/tdr_anvil/__init__.py
+++ b/src/azul/plugins/repository/tdr_anvil/__init__.py
@@ -169,14 +169,16 @@ def _version(self):
     datarepo_row_uuid_version = 4
     bundle_uuid_version = 10
 
-    def _count_subgraphs(self, source: TDRSourceSpec) -> int:
+    def count_bundles(self, source: TDRSourceSpec) -> int:
+        prefix = '' if source.prefix is None else source.prefix.common
         rows = self._run_sql(f'''
             SELECT COUNT(*) AS count
             FROM {backtick(self._full_table_name(source, BundleType.primary.value))}
+            WHERE STARTS_WITH(datarepo_row_id, {prefix!r})
             UNION ALL
             SELECT COUNT(*) AS count
             FROM {backtick(self._full_table_name(source, BundleType.supplementary.value))}
-            WHERE is_supplementary
+            WHERE is_supplementary AND STARTS_WITH(datarepo_row_id, {prefix!r})
         ''')
         return sum(row['count'] for row in rows)
 
diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py
index 320b0a4f1..2f10c564b 100644
--- a/src/azul/plugins/repository/tdr_hca/__init__.py
+++ b/src/azul/plugins/repository/tdr_hca/__init__.py
@@ -278,11 +278,14 @@ def _parse_drs_uri(self,
 
 class Plugin(TDRPlugin[TDRHCABundle, TDRSourceSpec, TDRSourceRef, TDRBundleFQID]):
 
-    def _count_subgraphs(self, source: TDRSourceSpec) -> int:
-        rows = self._run_sql(f'''
-            SELECT COUNT(*) AS count
-            FROM {backtick(self._full_table_name(source, 'links'))}
-        ''')
+    def count_bundles(self, source: TDRSourceSpec) -> int:
+        prefix = '' if source.prefix is None else source.prefix.common
+        query = f'''
+        SELECT COUNT(*) AS count
+        FROM {backtick(self._full_table_name(source, 'links'))}
+        WHERE STARTS_WITH(datarepo_row_id, {prefix!r})
+        '''
+        rows = self._run_sql(query)
         return one(rows)['count']
 
     def _list_bundles(self,