A method and system control for closing a plant application running on a manufacturing execution system (MES) application. The method includes the steps of providing to a set of classes, a custom shutdown rule to be customized at engineering time; defining, for certain classes belonging to the set of classis, certain shutdown rules with a set of actions to be performed by the MES application; notifying the closing request to the MES application; invoking the shutdown rules once for each object of the classes which have a defined shutdown rule; performing the actions defined in the invoked custom shutdown rules; by the MES application, closing or not closing the plant application according to the results of the invoked shutdown rules; by the MES application, notifying the PM launcher whether the plant application was closed or not.