In this work, we tuned the ion selectivity of a polyelectrolyte multilayer (PEM)-coated, cation-exchange membrane (CMX) in a membrane capacitive deionization (MCDI) process by carefully studying different operational modes, namely constant voltage (CV) and constant current (CC). The monovalent cation selectivity and its time-dependent behavior were monitored at different voltage and current values. Upon optimizing the current density (10 A/m2) and the number of polyelectrolyte bilayers (5.5) on the CMX membranes, a time-independent and nearly full monovalent cation selectivity was obtained for various feed solutions, provided a polycation-terminated PEM was applied. Furthermore, the selectivity values of several commercially available cation-exchange membranes were tested under the optimized conditions and compared with CMX and PEM-CMX, yielding the best performance for PEM-CMX, regardless the composition of feed solution. Before this optimization, this MCDI system showed a time-dependent selectivity, with a maximum of ρMgNa ≈3. The results were rationalized by applying an MCDI model based on the dynamic potential profile, describing the potential drops across the membrane and demonstrating a threshold for the current density.