In microbial fuel cells (MFC), oxidation and reduction processes occur simultaneously. In this study, the operating conditions affecting oxidation-reduction and electricity generation of MFC were optimized using the Taguchi Experimental Design model. Optimization was carried out for maximum power density, coulombic efficiency, azo dye removal and COD removal. With the determined optimum conditions (cathode pH of 3.0, cathode oxygen status of anaerobic, anode substrate of pre-treated, external resistance of 100 Ω, cathode electrode type of plain carbon, cathode electrode surface of 22 cm2, cathode conductivity of 20 µs/cm), 177.031 mW/m2 power density, 7.50% coulombic efficiency, 91.266% azo dye removal efficiency and 21.612% COD removal efficiency were obtained. From the Pareto analysis, it was determined that the power density, coulombic efficiency and COD removal efficiency were most affected by the substrate type at the anode, and the azo dye removal was most affected by the catholyte pH. With the polarization curve, it has been determined that the maximum power density is 145.11 mW/m2 and the internal resistance of the optimum MFC system is 243.3 Ω. The cyclic voltammogram performed with the optimum experiment was associated with oxidation and reduction reactions.