Long-term performance of capacitive deionization (CDI) and membrane-assisted capacitive deionization (MCDI) single cells equipped with the same pristine carbon xerogel (CX) electrodes configured as the anode and cathode was investigated. Unlike CDI, which was subject to performance degradation in a short period of time, MCDI showed performance preservation during the 50 h of operation due to its ability to mitigate charge leakage from parasitic electrochemical reactions that result in carbon oxidation. Differential capacitance measurements of the used CDI and MCDI electrodes revealed shifting of the potential of zero charge (EPZC) of the CDI anode from -0.1 to 0.4 V but only to 0.1 V for the MCDI anode. CDI and MCDI cells tested with electrodes having EPZCs at -0.1 and 0.5 V showed strongly contrasting results depending on the anode-cathode EPZC configuration. The MCDI cell configured with a 0.5 V EPZC cathode and -0.1 V EPZC anode displayed the best performance of all the tested cells, benefiting from increased counterion excess within the potential window, and the membrane was in-place to reject expelled co-ions from accessing the bulk.