Microbial fuel cells (MFCs) have been investigated as a promising renewable energy source, although harvesting energy from MFCs is not a simple task because of their low terminal voltage and output power. For an energy harvesting system (EHS) for MFC, controlling the MFC's operating point to track the maximum power point (MPP) is essential to maximize the harvested energy, but it requires a complex control system that consumes significant amount of energy. Although this control power is a critical factor because of its substantial impact on overall efficiency, it has been largely neglected. Furthermore, the transient of MFC reactor has not been taken into consideration enough for MPPT algorithms even though it could significantly affect the operation of such algorithms. In this paper, a net power positive EHS for MFC is proposed, which has a microcontroller that tracks the MPP using a novel power estimation method considering the dynamics of MFC reactor. The proposed EHS uses only a fraction of the harvested MFC power and was able to operate at a steady-state MPP without any external power. The experimental results show that the overall efficiency of the proposed system at MPP is 59.4% with a microcontroller power consumption of 8.67 μW.