Model Based System Engineering (MBSE) allows an optimized development of new mechatronic systems and/or functionalities. In this paper a MBSE approach is proposed where two control functionalities are applied to improve the dynamic performance of a Scara Robot. Acceleration feedback is used to increase vibration damping capacity and Iterative Learning Control is applied to reduce path errors. A simulation model combining Scara Robot mechanics, developed in Simcenter Amesim™ software from Siemens Digital Industries Software, and control loops, developed in Simulink, has been used to implement and evaluate the functionalities. Finally, both algorithms were implemented in a real Scara robot that was previously adapted to be controlled by a FAGOR CNC.