Benthic microbial fuel cells (BMFCs) are alternative energy sources that can power sensors underwater. However, their use underwater is limited by low conversion efficiencies of the low-voltage energy to higher voltages required by modern electronics. Additionally, BMFC systems detailed in the literature are incompatible with the deployment difficulties associated with underwater sensing. In this work, we present an optimal underwater scaling strategy combined with an integrated power management system. We successfully demonstrate the modular scale-up of BMFCs using in-line flyback converters that held the BMFC input voltage at an optimal cell potential of 0.35–0.5 V while directly increasing output voltage to 12 V. Two flyback converters could operate successfully on a single shared anode, delivering 16 mW of the BMFC power directly to a 12 V rechargeable battery at 77% efficiency. We show that the internal resistance of the BMFC and effective resistance of the power management system determine the transition from start up to stable BMFC operation for up to seventy days. These combined factors have not been demonstrated previously. Such a system allows for a broad range of BMFC underwater array configurations that are critical to the future integration of BMFCs with seafloor systems and sensors.