Sedimentary microbial fuel cells are promising harvesting systems generating powers as low as 10 μW, which is sufficient for powering underwater environmental sensors. This paper proposes a methodology and modeling to design a flyback converter in discontinuous conduction mode harvesting powers as low as 10th of μWs to maximize the harvested energy and boost its voltage to a minimum value required by sensors. Using a model validated experimentally, we figure out the converter loss contributors and balance them to maximize the power efficiency. We achieved 28% and 75%, efficiency with an input power of 10 μW and 30 μW respectively.