Microbial fuel cells (MFCs) are attracting considerable attention because they can produce renewable energy from organic matter. To extract useable energy from MFCs, a suitable energy harvester is needed that can store energy in a capacitor and increase the output voltage of the MFC. We present an ultra-low-power energy harvester specially designed for MFCs (UPEM) which can extract energy even from extremely low-power, inexpensive, and single MFCs. The minimum required input power from an MFC to UPEM for charging a supercapacitor to 3.3 V is only 2.09 mu W, and this value is two orders of magnitude lower than any input power reported for any energy harvester till date. UPEM is the first harvester that succeeded in obtaining almost realtime measurements of temperature and humidity, CO2 sensing, iBeacon (TM) transmission, and long-range wireless data transmission (>5 km) with a LoRa module at intervals shorter than 3 h, using a single MFC with a maximum power of 0.52 mW. These results show that UPEM can enable the realization of various applications of MFCs, such as their use in MFC-driven autonomous environmental sensing devices to measure greenhouse gases in remote off-grid locations.