Micro-Electro-Mechanical-Systems are complex structures, often involving nonlinearites of geometric and multiphysics nature, that are used as sensors and actuators in countless applications. Starting from fullorder representations, we apply deep learning techniques to generate accurate, efficient and real-time reduced order models to be used as virtual twin for the simulation and optimization of higher-level complex systems. We extensively test the reliability of the proposed procedures on micromirrors, arches and gyroscopes, also displaying intricate dynamical evolutions like internal resonances. In particular, we discuss the accuracy of the deep learning technique and its ability to replicate and converge to the invariant manifolds predicted using the recently developed direct parametrization approach that allows extracting the nonlinear normal modes of large finite element models. Finally, by addressing an electromechanical gyroscope, we show that the non-intrusive deep learning approach generalizes easily to complex multiphysics problems.