During the operation of a microbial bioelectrochemical system, charge balance must be maintained between the anode and the cathode. In an ideal scenario, the charge balance would be realized by the unhindered migration of H(+) or OH(-). At the same time, any kind of diffusion (crossover) between both electrode compartments should be avoided. However, as several studies have demonstrated, the experimental reality does not match this ideal picture. Crossover processes occur and H(+)/OH(-) migration only plays an inferior role in the charge-balancing ion transfer, which results in significant losses in the performance of the microbial bioelectrochemical system. This Minireview summarizes the conflict of selectivity versus mobility and discusses principle strategies to cope with the resulting constraints, including pH-static operation and the use of different separator materials and membrane-free systems. Finally, we show that every setup compromises either selectivity or mobility, and no apparent ideal solution currently exists.