Microbial fuel cells (MFC) are electrical devices that use microorganisms to convert soluble organic matter into energy in the form of hydrogen and electricity. In this work, MFCs were investigated for their ability to reduce the concentration of known fermentation inhibitors expected from emerging biomass fermentation industry. Specifically, the convesion of furfural, a xylose degradation product, and lignin degradation products such as vanillic acid and 4-hydroxybenzaldehyde was investigated. A new engineering design approach resulted in the high power densities and coulombic efficiencies for the MFC.  A 16S rRNA analysis was conducted to determine the composition of the unique exoelectrogenic microbial consortium enriched in the MFC. The consortium demonstrated broad substrate specificity, ability to handle high inhibitor concentrations with near complete removal, while maintaining long-term stability. This approach can lead to: 1) higher ethanol yields at high biomass loading, 2) improved water recycle and 3) electricity production to meet part of the biorefinery power needs.