Abstract: The present invention provides a microbial fuel cell power system based on a microbe-based fuel cell such as a benthic microbial fuel cell (BMFCs). In accordance with the present invention, one or more BMFCs can be connected to one or more batteries such as a nickel metal hybrid (NiMH) or sealed lead acid (SLA) battery and can be used to charge the batteries for long-term persistent underwater use. At any time, some of the connected batteries are being charged by the BMFC, while the others are being used to power a connected device. By using electrically isolated fuel cell converters, the batteries can be charged while in circuit. With non-isolated converters, pairs of batteries can be switched between offline charging and online discharging. The battery system can be controlled by a control system that comprises a microcontroller that periodically measures system voltages and currents, swaps the batteries being charged, and records the system results for post-mission analysis.