Microbial fuel cell (MFC) is an emerging technology for sustainable energy production. An MFC employs indigenous microorganisms as biocatalysts and can theoretically convert any biodegradable substrate into electricity, making the technology a viable solution for sustainable waste treatment or autonomous power supply. However, the electric energy currently generated from MFCs is not directly usable due to the low voltage and current output. Moreover, the output power can fluctuate significantly according to the operating conditions, which makes stable harvest of energy difficult. This paper presents an MFC energy harvesting scheme using a hysteresis controller and two layers of DC/DC converters. The proposed energy harvesting system can capture the energy from multiple MFCs at individually controlled operating point and at the same time form the energy into a usable shape.