Microbial fuel cells (MFCs) use bacteria as the catalysts to oxidize organic matter and generate electricity. This energy can be used to supply low power electronic systems. A power management unit between the MFCs and the load is required to adapt the voltage and control the operation. The low voltage and low power characteristics of MFCs prohibit the use of standard converter topologies since the threshold voltage of standard CMOS transistors in CMOS technology is higher than the output voltage of MFCs. A low-voltage start-up sub-circuit is required to charge a primary capacitor to supply the driver. A specific sub-circuit is also required to control the operation of MFCs for Maximum Power Point Tracking (MPPT) issues. An optimized Discontinuous Conduction Mode (DCM) autonomous flyback converter for energy harvesting is presented for ambient sources, like MFCs. The converter is designed, fabricated, and tested. An MPPT algorithm is integrated in the system to control the operation and to extract the maximum available power from the MFC. The converter is able of start and step-up MFC output voltage to a value higher than 3 V under load. The peak efficiency of the converter is 71.2%.