The increasing complexity of aeronautical systems, combined with the growing need for a more sustainable aviation, requires more efficient verification and validation workflows. In the current state of the art, the V-model development processes rely on Document-Based System Engineering and manually generated simulation models that are loosely coupled with the system architecture, leading to inconsistencies, poor traceability, and significant rework and higher costs when design changes occur. This thesis proposes a novel Model-Based System Engineering workflow for the automated virtual verification of complex aeronautical systems, developed in the context of the ODE4HERA project in the Clean Aviation initiative for the development of a Hybrid-Electric Regional aircraft.