diff --git a/sphinxcontrib/versioning/sphinx_.py b/sphinxcontrib/versioning/sphinx_.py
index 4fffcb114..6efe45dd0 100644
--- a/sphinxcontrib/versioning/sphinx_.py
+++ b/sphinxcontrib/versioning/sphinx_.py
@@ -7,6 +7,7 @@
 import sys
 
 from sphinx import application, locale
+from sphinx.deprecation import _ModuleWrapper
 from sphinx.cmd.build import build_main
 from sphinx.builders.html import StandaloneHTMLBuilder
 from sphinx.config import Config as SphinxConfig
@@ -182,8 +183,13 @@ def _build(argv, config, versions, current_name, is_root):
     :param str current_name: The ref name of the current version being built.
     :param bool is_root: Is this build in the web root?
     """
-    # Patch.
-    application.Config = ConfigInject
+
+    # patch, if there are deprecations, patch hidden module object
+    if isinstance(application, _ModuleWrapper):
+        application._module.Config = ConfigInject
+    else:
+        application.Config = ConfigInject
+
     if config.show_banner:
         EventHandlers.BANNER_GREATEST_TAG = config.banner_greatest_tag
         EventHandlers.BANNER_MAIN_VERSION = config.banner_main_ref
@@ -202,7 +208,6 @@ def _build(argv, config, versions, current_name, is_root):
     if config.overflow:
         argv += config.overflow
 
-    # Build.
     result = build_main(argv)
     if result != 0:
         raise SphinxError