Proton and electron transfer are of prime importance in development of microbial electrochemical cells. While electron transfer is primarily controlled by biology, proton transfer is controlled by process engineering and cell design. To develop commercially feasible technologies around the concept of a bioelectrochemical cell, real feedstocks have to be explored and associated limitations identified. In this study, proton transfer rate was quantified and its dependence on process parameters was investigated. A proton balance model was developed for a microbial electrolysis cell (MEC). The reaction system consisted of a biomass-derived pyrolytic aqueous stream as a substrate producing hydrogen in a flow-through MEC. The proton transfer rate increased with anode flow rate up to a maximum of 0.29 ± 0.01 moles/m2-hr, reaching a hydrogen production rate of 6.6 ± 0.59 L/L-day. Higher rates of hydrogen were achieved when cathode buffer served as the primary source of protons enabling a rate of 11.7 ± 0.2 L/L-day. Electrochemical impedance spectroscopy shows that anode impedance was limiting overall rate of hydrogen production. The analysis suggests that alleviating proton transfer limitations in the anode can result in improving hydrogen production approaching rates required for commercial consideration.