In this work, a low-temperature fabrication process of thin film encapsulation (TFE) with silicon nitride/chromium cap is proposed for large-size (750 μm x 300 μm) packaging of microelectromechanical systems (MEMS). A FEM model was developed to evaluate the shape of TFE as a function of the residual stress and the thickness of the sealing layer, providing useful guidelines for the fabrication process. The low temperature of 200 °C, which was used in the plasma-enhanced chemical vapor deposition of the silicon nitride capping layer, allowed an organic sacrificial material to be employed for the definition of the encapsulation area. Silicon nitride/chromium (1 μm/20 nm) bilayer was demonstrated to be successful to overcome the technological limitations that affect the creation of cap holes with size of ~2 μm on high topography substrates, as in the case of MEMS. Plasma focused ion beam (PFIB) and scanning electron microscopy (SEM) techniques were used in combination to gain deeper insight into the sealing process of cap holes. Specifically, a PFIB-SEM serial section procedure was developed, resulting to be a powerful tool to directly observe the sealing profile above cap holes. Hence, the presented results greatly contribute to overcome the main technological/reliability issues of TFE, paving the way for the widespread application of the proposed encapsulation methodology to the most used MEMS devices, as radio-frequency (RF) switches, transducers, actuators, sensors and resonators.