Bioelectrochemical systems (BES) are used to extract electrons from the phenolic and aromatic acid components via an electrogenic anode consortia. The primary product at the cathode evaluated is hydrogen, although other products including biofuels can be generated. Production of hydrogen using such a system is evaluated as a high efficiency process alternative. Removal of furfural, HMF, phenolics, acetate, naphthenic acids is reported with concomitant production of hydrogen. Improvements in current density and coulombic efficiency of the bioanode were studied by varying multiple operational parameters. Water recycle and energy efficiency improvements are important issues for emerging cellulosic biomass fermentation industry. The substrate specificity and stability of the consortia for treatment of an effluent from pyrolysis process will be discussed. This approach can lead to: 1) reduction in use of fossil derived hydrogen for upgrading, 2) higher fuel yield from biomass, 3) water recycle.