Electromechanical actuators (EMAs) are becoming increasingly attractive in the field of more electric aircraft because of their outstanding benefits, which include reduced fuel burn and maintenance cost, enhanced system flexibility, and improved management of fault detection and isolation. However, electromechanical actuation raises specific issues when being used for safety-critical aerospace applications like flight controls: huge reflected inertia to load, jamming-type failure, and increase of backlash with service due to wear and local dissipation of heat losses for thermal balance. This study proposes an incremental approach for virtual prototyping of EMAs. It is driven by a model-based system engineering process in order to enable simulation-aided design. Best practices supported by Bond graph formalism are suggested to develop a model’s structure efficiently and to make the model ready for use (or extension) by addressing the above mentioned issues. Physical effects are progressively introduced, and the realism of lumped-parameter models is increased step-by-step. In particular, multi-level component models are architected to ensure continuity between engineering activities. The models are implemented in the AMESim simulation environment, and simulation responses are given to illustrate how they can be used for preliminary sizing, control design, thermal balance verification, and faults to failure analysis. The proposed best practices intend to provide engineers with fast, reusable, and efficient means to assess performance virtually and enhance maturity, performance, and robustness.