diff --git a/src/app/rpmostree-compose-builtin-tree.c b/src/app/rpmostree-compose-builtin-tree.c
index b256b6b4..e308b6c9 100644
--- a/src/app/rpmostree-compose-builtin-tree.c
+++ b/src/app/rpmostree-compose-builtin-tree.c
@@ -915,6 +915,11 @@ impl_compose_tree (const char      *treefile_pathstr,
       }
   }
 
+  /* Destroy this now so the libdnf stack won't have any references
+   * into the filesystem before we manipulate it.
+   */
+  g_clear_object (&self->corectx);
+
   if (g_strcmp0 (g_getenv ("RPM_OSTREE_BREAK"), "post-yum") == 0)
     return FALSE;