In this article a new device based on 4 × 4 matrix micromachined resonating piezoelectric membranes used as DNA–DNA hybridization biosensor is proposed. This biosensor is operated in two fundamental different ways, namely integrated in a flow injection analysis (FIA) system and providing measurements by the “dip-and-dry” technique. After the fabrication and characterization phase of the micromachined resonating piezoelectric membranes, an appropriate FIA system for biosensing tests had to be developed. The biosensor functionality was validated in two ways: on the one hand the piezoelectric membranes have been used to measure the real-time kinetics of gold colloid adsorption, the whole matrix being integrated in the FIA system. The mass sensitivity of the device has been estimated to −3.6 Hz/pg which is by a factor of several hundreds better than of state-of-art values for piezoelectric mass-sensing devices. On the other hand, dip-and-dry technique has been used to measure the mass loading induced by the binding of streptavidin–conjugated gold nanoparticles to biotinylated target cDNA fixed onto the surface of the piezoelectric membranes. Measurement of resonant frequency of one piezoelectric membrane has been performed before and after adsorption of the streptavidin–conjugated gold nanoparticles and a 3.9 kHz shift of the resonant frequency has been recorded. These results indicate that micromachined piezoelectric membranes have real potential as micromechanical biosensors.