diff --git a/test/unit/data/test_galaxy_mapping.py b/test/unit/data/test_galaxy_mapping.py
index 709e1f049a9..2903c0ad915 100644
--- a/test/unit/data/test_galaxy_mapping.py
+++ b/test/unit/data/test_galaxy_mapping.py
@@ -661,7 +661,7 @@ class TestMappings(BaseModelTestCase):
 
         self.new_hda(h1, name="1")
         self.new_hda(h2, name="2")
-        self.session().flush()
+        self.session().commit()
         # _next_hid modifies history, plus trigger on HDA means 2 additional audit rows per history
 
         h1_audits = get_audit_table_entries(h1)
@@ -672,7 +672,13 @@ class TestMappings(BaseModelTestCase):
         h1_latest = get_latest_entry(h1_audits)
         h2_latest = get_latest_entry(h2_audits)
 
+        # In galaxy, HistoryAudit.prune() executes in the context of a separate thread, where it
+        # starts and commits a new transaction, closing a scoped session on exit. Thus, here we
+        # should end the current transaction (via rollback) and add the History objects to a new
+        # session, as the previous one will be closed.
+        self.session().rollback()
         model.HistoryAudit.prune(self.session())
+        self.session().add_all([h1, h2])
 
         h1_audits = get_audit_table_entries(h1)
         h2_audits = get_audit_table_entries(h2)