This work reports a method to select the optimal working frequency in transversal bulk resonator acoustophoretic devices by electrical impedance measurements. The impedance spectra of acoustophoretic devices are rich in spurious resonance peaks originating from different resonance modes in the system not directly related to the channel resonance, why direct measurement of the piezoelectric transducer impedance spectra is not a viable strategy. This work presents, for the first time, that the resonance modes of microchip integrated acoustophoresis channels can be identified by sequentially measuring the impedance spectra of the acoustophoretic device when the channel is filled with two different fluids and subsequently calculate the Normalized Differential Spectrum (NDS). Seven transversal bulk resonator acoustophoretic devices of different materials and designs were tested with successful results. The developed method enables a rapid, reproducible and precise determination of the optimal working frequency.