Microbial fuel cells (MFCs) are emerging as a novel technology with a great potential to reduce the costs of wastewater treatment. Their most studied application is organic carbon removal. One of the parameters commonly used to quantify the performance of these cells is the Coulombic efficiency, i.e., the electron recovery as electricity from the removed substrate. However, the "inefficiencies" of the process have never been fully identified. This study presents a method that uses the combination of electrochemical monitoring, chemical analysis, and a titration and off-gas analysis (TOGA) sensor to identify and quantify the sources of electron loss. The method was used successfully to close electron, carbon, and proton balances in acetate and glucose fed microbial fuel cells. The method revealed that in the case that a substrate is loaded as pulses carbon is stored inside the cells during initial high substrate conditions and consumed during starvation, with up to 57% of the current being generated after depletion of the external carbon source. Nile blue staining of biomass samples revealed lipophilic inclusions during high substrate conditions, thus confirming the storage of polymeric material in the bacterial cells. The method also allows for indirect measurement of growth yields, which ranged from 0 to 0.54 g biomass-C formed per g substrate-C used, depending on the type of substrate and the external resistance of the circuit.