Cyber-physical systems (CPS) are gaining a steadily increasing share of critical ecosystems and infrastructures. CPS can also be found inside autonomous vehicles, aircraft, health care equipment, the smart grid, and smart factories. Components of CPS combine analog parts such as sensors and actuators with digital control and networked software systems. The design of these systems requires the integration of a high number of system components from many different disciplines. Security and performance are of crucial importance, in the complete development-operation continuum. Tightly entangled, security and performance are not always compatible. Our objective is to define an adequate methodology to model and verify CPS with security requirements, considering trade-offs between performance, security, development and runtime.