Microbial Fuel Cells (MFCs) use biodegradable substrates, such as wastewater and marine sediments to generate electrical energy. To harvest more energy from an MFC, power electronic converters have recently been used to replace resistors or charge pumps, because they have superior controllability on MFC's operating point and higher efficiency in energy storage for different applications. Conventional diode-based energy harvesters suffer from low efficiency because of the energy losses through the diode. Replacing the diode with a MOSFET can reduce the conduction loss, but it requires an isolated gate signal to control the floating secondary MOSFET, which makes the control circuitry complex. This study presents a new MFC energy harvesting regime using a synchronous flyback converter, which implements a transformer-based harvester with much simpler configuration and improves harvesting efficiency by 37.6% compared to a diode based boost converter, from 33.5% to 46.1%. The proposed harvester was able to store 2.27 J in the output capacitor out of 4.91 J generated energy from the MFC, while the boost converter can capture 1.67 J from 4.95 J. (C) 2013 Elsevier B.V. All rights reserved.