diff --git a/lib/galaxy/tool_shed/galaxy_install/install_manager.py b/lib/galaxy/tool_shed/galaxy_install/install_manager.py
index 12a284cf045..cee14887f0d 100644
--- a/lib/galaxy/tool_shed/galaxy_install/install_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/install_manager.py
@@ -188,6 +188,8 @@ class InstallRepositoryManager:
             sample_files = irmm_metadata_dict.get("sample_files", [])
             tool_index_sample_files = stdtm.get_tool_index_sample_files(sample_files)
             tool_data_path = self.app.config.tool_data_path
+            # Used to be created as a side effect of install_tool_data_tables; that no longer runs for non-DM repos.
+            os.makedirs(tool_data_path, exist_ok=True)
             tool_util.copy_sample_files(tool_data_path, tool_index_sample_files, tool_path=tool_path)
             sample_files_copied = [str(s) for s in tool_index_sample_files]
             repository_tools_tups = irmm.get_repository_tools_tups()
diff --git a/test/integration/test_repository_operations.py b/test/integration/test_repository_operations.py
index 33a0e5e9527..3c9a415f7e6 100644
--- a/test/integration/test_repository_operations.py
+++ b/test/integration/test_repository_operations.py
@@ -1,4 +1,5 @@
 import os
+import xml.etree.ElementTree as ET
 from collections import namedtuple
 
 from sqlalchemy import select
@@ -62,13 +63,14 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC
         self.uninstall_repository(*repo)
 
     def test_non_data_manager_install_skips_data_table_registration(self):
-        """Non-Data-Manager repos must not register data tables on install."""
+        """Non-Data-Manager repos must not persist data table entries in shed_tool_data_table_conf.xml."""
         non_dm_repo = ("devteam", "bwa", "051eba708f43")
         non_dm_table_names = {"bwa_indexes", "bwa_mem_indexes"}
         self.install_repository(*non_dm_repo)
-        registered = set(self._app.tool_data_tables.data_tables.keys())
+        shed_conf = self._app.config.shed_tool_data_table_config
+        registered = {t.get("name") for t in ET.parse(shed_conf).getroot().findall("table")}
         leaked = non_dm_table_names & registered
-        assert not leaked, f"Unexpected data tables registered by non-DM repo: {sorted(leaked)}"
+        assert not leaked, f"Unexpected data tables in {shed_conf}: {sorted(leaked)}"
 
     def test_repository_update(self):
         response = self._install_repository(revision=REVISION_4, version="0.0.3", allow_upgraded=True)[0]