This paper proposes a battery-compatible electronic interface based on a general purpose lock-in amplifier (LIA) capable of recovering input signals up to the MHz range. The core is a novel ASIC fabricated in 1.8 V 0.18 µm CMOS technology, which contains a dual-phase analog lock-in amplifier consisting of carefully designed building blocks to allow configurability over a wide frequency range while maintaining low power consumption. It operates using square input signals. Hence, for battery-operated microcontrolled systems, where square reference and exciting signals can be generated by the embedded microcontroller, the system benefits from intrinsic advantages such as simplicity, versatility and reduction in power and size. Experimental results confirm the signal recovery capability with signal-to-noise power ratios down to −39 dB with relative errors below 0.07% up to 1 MHz. Furthermore, the system has been successfully tested measuring the response of a microcantilever-based resonant sensor, achieving similar results with better power-bandwidth trade-off compared to other LIAs based on commercial off-the-shelf (COTS) components and commercial LIA equipment.