We report an integrated experimental and simulation study of ammonia recovery using microbial electrolysis cells (MECs). The transport of various species during the batch-mode operation of an MEC was examined experimentally and the results were used to validate the mathematical model for such an operation. It was found that, while the generated electrical current through the system tends to acidify (or basify) the anolyte (or catholyte), their effects are buffered by a cascade of chemical groups such as the NH3/NH4(+) group, leading to relatively stable pH values in both anolyte and catholyte. The transport of NH4(+) ions accounts for ~90% of the total current, thus quantitatively confirming that the NH4(+) ions serve as effective proton shuttles during MEC operations. Analysis further indicated that, because of the Donnan equilibrium at cation exchange membrane-anolyte/catholyte interfaces, the Na(+) ion in the anolyte actually facilitates the transport of NH4(+) ions during the early stage of a batch cycle and they compete with the NH4(+) ions weakly at later time. These insights, along with a new and simple method for predicting the strength of ammonia diffusion from the catholyte toward the anolyte, will help effective design and operation of bioeletrochemical system-based ammonia recovery systems.