In this paper, several physical phenomena that are usually not taken into account in MEMS simulations are considered for the simulation of a MEMS xylophone bar magnetometer. These phenomena are the temperature dependency of the material properties, the strong coupling between various fields of physics (thermal, electric and mechanical) and the stress produced by the change of temperature inside the structure. It is shown that the temperature dependency of the material properties has a relatively small influence whereas the pre-stress has a significant one. Because of the pre-stressed state, the deformation of the bar at the fundamental frequency is not a typical first mode vibration but it exhibits additional waves between the linkages, where the bar is stressed, which significantly decrease the amplitude of the deflection.