Microbial fuel cells (MFC) generate electricity using bacteria and they have been investigated as promising renewable energy source. Although they generate low power compared to other fuel cells, they have been used to replace batteries in powering remote wireless sensors. Energy harvesting circuits are used to collect energy from MFCs, therefore, they need to be able to store the harvested energy and be ecient in order to use most of the MFC available power. Power electronics converters can be used to harvest MFC energy eciently and the harvested energy is typically stored in a capacitor or a battery. Power converters can be also used to control the operating point of the MFC reactor to harvest the maximum available power at the operating point, maximum power point (MPP), that gives the maximum available power. This dissertation is focused on improving the use of power electronics converters in MFC energy harvesting in terms of reliability and eciency. It also investigates the eect of using power electronics converters on the reactor performance and conditions. The reliability of the energy harvesting circuit was increased by proposing an algorithm that can detect and avoid voltage overshoot in MFCs. Voltage overshoot happens during energy harvesting, where the reactor terminal voltage collabses because of high currents, which signicantly aect MFC energy harvesting. The proposed algorithm is based on extremum seeking (ES) algorithm, where it can track MPP in the normal conditions and can detect voltage overshoot once it happens. Then, the algorithm tries to nd an operating point that is far from the voltage overshoot region. Energy harvesting from MFC using power electronics converters imposes current ripple on MFC reactor because of their switching behavior, and such current ripple can have an eect on other fuel cells such as PEMFC. The experimental results showed that there is no signicant eect of power electronics converters current ripple on the MFC reactor performance in terms of voltage, power, and longevity. It was also shown that the conditions of the reactor such as pH, dissolved oxygen (DO), electrical conductivity (EC), and oxidation reduction potential (ORP) are not aected by that current ripple. Finally, a self-powered energy harvesting system (EHS) is proposed. That system has a microcontroller that can be used to track MPP using a proposed power estimation method that saves substantial power that is normally consumed to measure the power. EHS is designed to use only fraction of the MFC harvested power in order to make a self-sustainable system. The experimental results show that the eciency of the proposed system is up to 59.4% with a microcontroller power consumption of 8.67muW with a 119muW MFC reactor.