The asymmetric resonance response in electro-thermal piezoresistive cantilever resonators causes a need of an optimization treatment for taking parasitic actuation-sensing effects into account. An electronic reference circuit for signal subtraction, integrated with the cantilever resonator has the capability to reduce the effect of parasitic coupling. Measurement results demonstrated that a symmetric amplitude shape (Lorentzian) and an optimized phase characteristic (i.e., monotonically decreasing) were successfully extracted from an asymmetric resonance response. With the monotonic phase response, real-time frequency tracking can be easier to implement using a phase-locked loop (PLL) system. In this work, an electro-thermal piezoresistive cantilever resonator functionalized with self-assembled monolayers of chitosan-covered ZnO nanorod arrays as sensitive layers has been investigated under different relative humidity (rH) levels. Enhancement of resonance phase response has been demonstrated by implementing the reference signal subtraction. Subsequently, a lock-in amplifier integrated with PLL system (MFLI, Zurich Instruments, Zurich, Switzerland) was then employed for continuously tracking the resonant frequency. As a result, we find a good correlation of frequency shift (∆f0) with change in rH monitored using a commercial reference sensor.