Adaptive manufacturing systems achieve intelligence and adaptation capabilities through the close interaction between mechanics, electronics, control and software engineering. Mechatronic design of intelligent manufacturing behaviours is of paramount importance for the final performances of complex systems and requires deep integration between mechanical and control engineering. Virtual Commissioning environments offer engineers new opportunities for the design of complex intelligent behaviours and for the enhancement of the performance of adaptive manufacturing systems. This paper discloses a systematic design method focused on interdisciplinary behavioural simulations: Virtual Commissioning tools are used to virtually explore new solution spaces for an effective mechatronic optimization. The results, achieved by applying the method in reengineering a module of an automotive sensor manufacturing line, are finally presented.