The resolution of low-frequency resistance noise measurements can be increased by amplitude modulation, shifting the spectrum of the resistance fluctuations away from the 1/f noise contributed by measurement instruments. However, commercial lock-in amplifiers used for de-modulating the fluctuations exhibit a problematic 1/f noise contribution, which imposes a hard lower limit on the relative resistance noise that can be detected. We replace the lock-in amplifier hardware by equivalent digital signal processing performed using open-source software and off-the-shelf data acquisition systems. Compared to previous implementations of the lock-in principle, our solution offers real-time preview capabilities and is resource-efficient for long acquisition times at high sampling rates. Importantly, compared to high-end commercial lock-in instruments, our system offers superior low-frequency noise performance with a reduction of the voltage power spectral density by about two orders of magnitude.