Microbial fuel cells (MFCs) are emerging as a promising alternative renewable energy source, especially for remote monitoring applications. Due to its low voltage and power output, MFCs are unable to directly drive most commercial electronic devices. A power management system (PMS) is needed to accumulate MFC energy first and then drive the load intermittently. In this study, a transformer-based PMS is proposed, which is able to function under a lower voltage input than other available MFC PMS designs. Two super-capacitors are included in the proposed PMS. The first is analytically optimized to maximize the average harvested power, while the second is selected based on the energy required to drive a given load. A continuous-mode MFC was built and used to successfully drive an IEEE 802.15.4 wireless sensor system using the proposed PMS. Experimental results showed that the proposed PMS worked well under a very low input voltage (0.18V). The configuration of two super-capacitors and a transformer in this transformer-based PMS provides more flexibility in harvesting power from MFCs.