A model azo dye, methyl orange (MO), was reduced through in situ utilization of the electrons derived from the anaerobic conversion of organics in a microbial fuel cell (MFC). The MO reduction process could be described by a pseudo first-order kinetic model with a rate constant of 1.29 day(-1). Electrochemical impedance spectroscopic analysis shows that the cathode had a high polarization resistance, which could decrease the reaction rate and limit the electron transfer. To improve the MO reduction efficiency, the cathode was modified with redox mediators to enhance the electron transfer. After modification with thionine, the polarization resistance significantly decreased by over 50%. As a consequence, the MO decolorization rate increased by over 20%, and the power density was enhanced by over three times. Compared with thionine, anthraquinone-2, 6-disulfonate modified cathode has less positive effect on the MFC performance. These results indicate that the electrode modification with thionine is a useful approach to accelerate the electrochemical reactions. This work provides useful information about the key factors limiting the azo dye reduction in the MFC and how to improve such a process.