Nowadays, the constantly changing market demands make modern automation systems offer more strict flexibility and efficiency requirements as energy efficiency, performance optimization and tolerance to process or controllers faults… The introduction of reconfiguration mechanisms within production automation systems allow meeting some of these requirements but, at the same time, they lead more complex design and implementation of the automation system. This paper explores the advantages of Model Driven Engineering techniques to manage such complexity. The proposed approach is based on two well spread standards in the automation field: AutomationML and IEC 61131-3 which have a Markup Language notation (AML and PLCopen XML respectively).