diff --git a/plinth/__main__.py b/plinth/__main__.py
index 09d062ff2..8d94b9415 100644
--- a/plinth/__main__.py
+++ b/plinth/__main__.py
@@ -102,8 +102,17 @@ def run_post_init_and_setup():
     """Run post-init operations on the apps and setup operations."""
     app_module.apps_post_init()
     frontpage.add_custom_shortcuts()
+
+    # Handle app version updates.
     setup.run_setup_on_startup()  # Long running, retrying
 
+    # Handle packages that have been updated else where that need a re-run of
+    # setup.
+    setup.on_dpkg_invoked()
+
+    # Handle packages that have a pending configuration file prompt.
+    setup.on_package_cache_updated()
+
 
 def main():
     """Initialize and start the application"""