The work is devoted to the study of a MEMS resonator dynamics under the action of phase-locked and automatic gain control loops. Particular attention is directed to the study of the nonlinearity factor of the resonator elastic restoring force. It was found that the determination of control system parameters based on the stability analysis of the operating resonant mode, in the general case, does not provide the required phase adjustment and stabilization of the oscillation amplitude. Stable multifrequency modes of oscillations are found, an analytical study of the mechanisms of their appearance and evolution is carried out under variation of the key parameters of the system. The real regions of the control system stable operation are determined (which do not coincide, as was found, with the regions of stability of the operating resonant mode, due to the presence of hidden attractors in the phase space of the system). A methodology has been developed for identifying such areas of stable operation. A significant complication of the structure of possible motions in the system with an increase in the Q-factor of the resonator is revealed.