A laboratory‐scale H‐shaped Pseudomonas catalyzed microbial fuel cell (MFC) was investigated for its performance in decolourizing synthetic wastewater containing azo dyes. The azo‐dyes investigated in this study were methyl orange (MO), congo red, reactive blue 172 (RB), reactive yellow 145, and reactive red 2. Among the azo dyes in anode chamber MO resulted in the highest power density (4100 μW m−2) with graphite electrodes and a decolourization efficiency of 94%. The azo bonds were cleaved in all the dyes tested, and their metabolites in the anolytes were characterized by UV‐visible spectral and HPLC analyses. To reduce the internal resistance of MFC and maximize the power density, different metal salt doped graphite epoxy composites) were tested. In the case of azo dyes MO and RB, the power output increased substantially (almost 1.2 fold) when using Mn2+—GECE compared to graphite block. © 2016 American Institute of Chemical Engineers Environ Prog, 35: 1623–1628, 2016