This paper proposes a new methodology to conduct commissioning activities for Basic Nuclear Facility (BNF) based on the implementation of a Model Based System Engineering (MBSE) approach coupled with theoretical foundations concerning the commissioning processes and the feedback of experience inherited from previous projects. The methodology illustrates the benefits of the MBSE to take into account the interfaces between the stakeholders, the building, equipment and processes and the different constraints related to the type of facility (safety and security requirements). The methodology is supported by two industrial nuclear projects and has allowed the elaboration of an innovative tests and trials program that will open the route to the early V&V applications that turn into a significant reduction of extra costs occurring in the case of commissioning projects.