A method for fabricating a low frequency quartz resonator includes metalizing a top-side of a quartz wafer with a metal etch stop, depositing a first metal layer over the metal etch stop, patterning the first metal layer to form a top electrode, bonding the quartz wafer to a silicon handle, thinning the quartz wafer to a desired thickness, depositing on a bottom-side of the quartz wafer a hard etch mask, etching the quartz wafer to form a quartz area for the resonator and to form a via through the quartz wafer, removing the hard etch mask without removing the metal etch stop, forming on the bottom side of the quartz wafer a bottom electrode for the low frequency quartz resonator, depositing metal for a substrate bond pad onto a host substrate wafer, bonding the quartz resonator to the substrate bond pad, and removing the silicon handle.