A new concept for a precise compensation of the static capacitance of piezoelectric silicon-based micromembranes is proposed. Combining analog and digital field-programmable gate array hardware elements with specific software treatment, this system enables the parallel excitation and detection of the resonant frequencies (and the quality factors) of matrices of piezoelectric micromembranes integrated on the same chip. The frequency measurement stability is less than 1 ppm (1-2 Hz) with a switching capability of 4 micromembranes/sec and a measurement bandwidth of 1.5 MHz. The real-time multiplexed tracking of the resonant frequency and quality factor on several micromembranes is performed in different liquid media, showing the high capability of measurement on dramatically attenuated signals. Prior to these measurements, calibration in air is done making use of silica microbeads successive depositions onto piezoelectric membranes surface. The mass sensitivity in air is, thus, estimated at, in excellent agreement with the theoretical corresponding value.