This work presents the development of an automatic and customized measuring system employing sigma-delta analog-to-digital converters and transimpedance amplifiers for precise measurements of voltage and current signals generated by microbial fuel cells (MFCs). The system can perform multi-step discharge protocols to accurately measure the power output of MFCs, and has been calibrated to ensure high precision and low noise measurements. One of the key features of the proposed measuring system is its ability to conduct long-term measurements with variable time steps. Moreover, it is portable and cost-effective, making it ideal for use in laboratories without sophisticated bench instrumentation. The system is expandable, ranging from 2 to 12 channels by adding dual-channel boards, which allows for testing of multiple MFCs simultaneously. The functionality of the system was tested using a six-channel setup, and the results demonstrated its ability to detect and distinguish current signals from different MFCs with varying output characteristics. The power measurements obtained using the system also allow for the determination of the output resistance of the MFCs being tested. Overall, the developed measuring system is a useful tool for characterizing the performance of MFCs, and can be helpful in the optimization and development of sustainable energy production technologies.