A recent trend in microfluidic microbial fuel cells (MFCs) is to exclude a separation membrane, instead, relying on the physics of laminar flow to maintain isolation between anode and cathode compartments. To avoid solution crossover, the electrodes may be separated by distances of several millimeters, but this negatively affects the internal resistance and undermines a prime advantage of microscale MFCs. Therefore, we propose a facile method for in situ synthesis of a micromembrane that supports sub-millimeter electrode spacing. Membrane synthesis in situ reduces device fabrication complexity, and the proposed design avoids electrode contamination during its synthesis. Comparing results to a state-of-the-art membraneless MFC with 6 mm inter-electrode distances, the sub-millimeter membrane MFC under comparable flow conditions had an internal resistance that was 60% lower, power and current densities that were respectively 45% and 290% higher, and acetate conversion efficiencies that were 8 times higher. The enhanced flow stability provided stable operation under imbalanced flow conditions and delivered continuous increases to power density of up to 30% for flow rate increases of 100 times over baseline levels. As a result, maximum outputs obtained were 660 mW m⁻¹ and 3.5 A m⁻¹. These are the highest reported for microfluidic MFCs using pure culture bacteria, which advances the goal of competing with mainstream MFC formats.