Here, we expose the influence of surface roughness on the dynamics of electromagnetic nano-resonators. To this end, the continuum field equations of an electromechanical nano-resonator subjected to an external magnetic flux are formulated. The developed model considers surface integrity, including surface roughness, waviness, and altered layer. Also, the influence of residual stresses of the extreme surfaces of the resonator is incorporated in the proposed model. It was revealed that the surface roughness significantly tailors the dynamic stability of the resonator, as the voltage that onsets the pull-in instability of the resonator decreases as the surface roughness increases, which thus indicates the necessity of particular calibrations of nano-resonators for surface roughness. To investigate the problem and the effect of factors such as magnetic field intensity, roughness, and beam surface thickness on the pull-in voltage, we have performed an analysis using the Taguchi method and analysis of variance. The results show that the intensity of the magnetic field has the most significant effect on pull-in voltage. Also, the more accurate results show on the resonance frequency; with the increase of the input voltage to the beam, the impact of increasing the intensity of the magnetic field and other factors increases. The rest of the paper proposes a linear and non-linear model to express the pull-in voltage according to the investigated factors.