Abstract: Ion exchange membranes represent the main core of a number of separation processes such as electrodialysis, diffusion dialysis and Donnan dialysis, among others, at which the key role of these membranes is to control the transport of ionic species and their selective separation simultaneously. However, the ion exchange capacity, selective separation, stability and durability of ion exchange membranes in separation processes are especially limited under the use of natural feedwaters due to their heterogeneous and multivalent ionic composition, which leads to several fouling issues. This effect provokes a clear undesirable evolution with time in the initial membrane properties and characteristics, thus significantly decreasing the overall process performance in several applications. As a consequence, not only a further understanding of the fouling mechanisms and the interactions between foulant(s) and membrane(s) is crucial, but also development of adequate membrane cleaning protocols to alleviate the fouling impact after prolonged operations. Therefore, the aim of the present review is to define efficient membrane cleaning strategies to control and mitigate the impacts of fouling phenomena on ion exchange membranes in separation processes, paying special attention to the type of membrane, its characterization (before and after cleaning) and the target application. Herein, promising membrane cleaning approaches reported in the recent years are summarized and discussed. Alternative physical, chemical and mechanical cleanings (or their combination) can be considered, even though the control of the number of cleaning cycles, cleaning conditions and combination of cleaning approaches seem to be essential to achieve an optimum global cleaning efficiency. To sum up, although further research in understanding the role of fouling in material stability and degradation after cleaning is still needed, this review provides novel insights into the definition of the most appropriate membrane cleaning strategy in different ion exchange membrane separation processes.