diff --git a/scripts/upgrade b/scripts/upgrade
index 413e1c5..1b5bdd2 100644
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -122,11 +122,28 @@ if [ "$upgrade_type" == "UPGRADE_APP" ]
 then
   ynh_script_progression --message="Upgrading source files..." --weight=2
 
+  # Create a temporary directory
+  tmpdir="$(mktemp -d)"
+
+  # Backup the config file and local plugins in the temp dir
+  cp -a "$final_path/config/config.json" "$tmpdir/config.json"
+  cp -ar "$final_path/plugins" "$tmpdir/plugins"
+
+  # Remove the app directory securely
+  ynh_secure_remove --file="$final_path"
+
   if [ "$version" = "Enterprise" ]; then
-    ynh_setup_source --dest_dir="$final_path" --source_id="enterprise" --keep="$final_path/plugins $final_path/config/config.json"
+    ynh_setup_source --dest_dir="$final_path" --source_id="enterprise"
   elif [ "$version" = "Team" ]; then
-    ynh_setup_source --dest_dir="$final_path" --source_id="$YNH_ARCH" --keep="$final_path/plugins $final_path/config/config.json"
+    ynh_setup_source --dest_dir="$final_path" --source_id="$YNH_ARCH"
   fi
+
+  # Copy the admin saved settings and plugins from tmp directory to final path
+  cp -a "$tmpdir/config.json" "$final_path/config/config.json" 
+  cp -ar --no-clobber "$tmpdir/plugins" "$final_path/"
+
+  # Remove the tmp directory securely
+  ynh_secure_remove --file="$tmpdir"
 fi
 
 chmod 750 "$final_path"