After long-term electrodialysis, cleaning the membranes is crucial to extend their lifetime. In this work, we evaluate the effects of a three-stage chemical cleaning on electrochemical and structural properties of anion- and cation-exchange membranes. Membranes used in the electrodialytic treatment of a synthetic effluent from the cyanide-free brass electrodeposition were cleaned using 0.1, 0.5 and 1.0 mol·L−1 NaOH solutions. The electrochemical behavior of the membranes was evaluated after each cleaning step by chronopotentiometry. Additionally, changes in the membrane structure and composition were analyzed by FTIR-ATR and SEM/EDS. While the membranes undergo a decline in some electrochemical features after the electrodialysis process, the cleaning with 0.1 mol·L−1 NaOH showed to be the most effective in recovering the properties characteristic of the virgin membranes: the limiting current density increased by 84% after the cleaning, whereas the ohmic and overlimiting resistances decreased by 47% and 55%, respectively. In contrast, the 0.5 and 1.0 mol·L−1 NaOH solutions degraded the membranes and reduced their fraction of conductive area, especially for the anion-exchange one. This favored fouling/scaling occurrence, as noticed by a prominent increase in the potential drop of the anion-exchange membrane. FTIR-ATR and SEM/EDS analyses confirmed fouling/scaling, as well as degradation of the ion-exchange membranes.