Microbial electrosynthesis (MES) provides a sustainable route for the conversion of CO2 and electricity into acetate and other organics. The conversion of CO2 takes place at a biologically active cathode (‘biocathode’), which is typically separated from the anode by an ion exchange membrane. Since both charged and uncharged species participate in the reaction, understanding the transport of these species through the membrane, and how this depends on the type of membrane, is of key importance. We develop a theory for ion mass transport and conversion in these types of microbial electrochemical cells. The theory includes ion transport, acid-base reactions, as well as electrochemical reactions at the electrodes. We first analyze a cell configuration including three compartments, in which the acetate recovery compartment in the middle is separated from the outer compartments by one cation exchange membrane and one anion exchange membrane, and we compare with experimental data from literature. Analysis of ion transport across the ion exchange membranes revealed that acetic acid/acetate and carbonic acid/bicarbonate species were used as proton shuttles between the catholyte compartment and the recovery compartment. We also analyzed a system including a bipolar membrane (BPM). Our results showed that a commonly made assumption that in BPMs the charge is solely carried by protons and hydroxyl ions, produced inside the BPM, is not generally correct. In our calculation charge is mainly carried by protons in the cation exchange layer of the BPM, while bisulphate and sulphate ions carry the charge in the anion exchange layer. In conclusion, we show that the ions which participate in acid-base reactions have to be considered in detail to describe and explain ion transport in MES cells and in the elements thereof such as BPMs.