The increasing complexity of the medical regulatory environment and the inherent complexity of medical devices, especially due to the increased use of connected devices and embedded control software, impose adoption of new methods and tools for the system design, safety and security analyses. In this paper, we propose a method and an associated toolchain to couple model-based system engineering and safety/security analyses at the design phase of medical devices. The method is compliant with ANSI/AAMI/ISO TIR57 safety and security guidance, and compatible with INCOSE Biomedical-Healthcare Model-Based Systems Engineering works. The toolchain is based on a system architecture modelling tool and supports medical device domain specific reference architecture, as well as tools for safety and security risk analyses. The proposed method and toolchain are illustrated by considering a RGB’s TOF-CUFF monitor device analyzed in the scope of the AQUAS project as a medical device use case.