diff --git a/src/app.py b/src/app.py
index 8b6e38d11..018c339e7 100644
--- a/src/app.py
+++ b/src/app.py
@@ -1996,7 +1996,10 @@ ynh_app_config_run $1
             }
         )
         app_script_env = _make_environment_for_app_script(app)
-        env.update(app_script_env)
+        # Note that we only need to update settings wich are not already set
+        # The settings from config panel should be keep as it is
+        app_script_env.update(env)
+        env = app_script_env
 
         ret, values = hook_exec(config_script, args=[action], env=env)
         if ret != 0: