diff --git a/jupyter_server/serverapp.py b/jupyter_server/serverapp.py
index 3dedd5634..bf375cbef 100644
--- a/jupyter_server/serverapp.py
+++ b/jupyter_server/serverapp.py
@@ -2724,7 +2724,11 @@ def initialize(
         self._init_asyncio_patch()
         # Parse command line, load ServerApp config files,
         # and update ServerApp config.
+        # preserve jpserver_extensions, which may have been set by starter_extension
+        # don't let config clobber this value
+        jpserver_extensions = self.jpserver_extensions.copy()
         super().initialize(argv=argv)
+        self.jpserver_extensions.update(jpserver_extensions)
         if self._dispatching:
             return
         # initialize io loop as early as possible,