Microbial fuel cells (MFCs) are renewable and sustainable energy sources that can be used for various applications. The MFC output power depends on its biochemical conditions as well as the terminal operating points in terms of output voltage and current. There exists one operating point that gives the maximum possible power from the MFC, maximum power point (MPP), for a given operating condition. However, this MPP may vary and needs to be tracked in order to maintain the maximum power extraction from the MFC. Furthermore, MFC reactors often develop voltage overshoots that cause drastic drops in the terminal voltage, current, and the output power. When the voltage overshoot happens, an additional control measure is necessary as conventional MPPT algorithms will fail because of the change in the voltage-current relationship. In this paper, the extremum seeking (ES) algorithm was used to track the varying MPP and a voltage overshoot avoidance (VOA) algorithm is developed to manage the voltage overshoot conditions. The proposed ES-MPPT with VOA algorithm was able to extract 197.2 mJ during 10-min operation avoiding voltage overshoot, while the ES MPPT-only scheme stopped harvesting after only 18.75 mJ because of the voltage overshoot happened at 0.4 min. (C) 2016 Elsevier B.V. All rights reserved.