This study investigates the influence of anode and cathode size and arrangement on hydrogen production in a membrane-less flat-plate microbial electrolysis cell (MEC). Protein measurements were used to evaluate microbial density in the carbon felt anode. The protein concentration was observed to significantly decrease with the increase in distance from the anode-cathode interface. Cathode placement on both sides of the carbon felt anode was found to increase the current, but also led to increased losses of hydrogen to hydrogenotrophic activity leading to methane production. Overall, the best performance was obtained in the flat-plate MEC with a two-layer 10 mm thick carbon felt anode and a single gas-diffusion cathode sandwiched between the anode and the hydrogen collection compartments.