During the last decades, the interest of using ion-exchange membranes (IEMs) in electrodialysis (ED) technologies has emerged in wastewater treatment, drinking water and process water production as well as food industry and more recently in processes of energy conversion and storage. Like in all membrane technologies, the problem of fouling is one of the limitative phenomena of IEM efficiency and lifetime. It mainly leads to an increase in electrical resistance of ED stacks and consequently to increase operating and membrane replacement costs, which directly affects the cost of the final product. In food industry, the composition of the treated solutions and beverages is most often complex and rich in several organic and inorganic compounds which further increases the risks and effects of fouling. Hence, a better knowledge and understanding of IEM fouling phenomena is not only the key to solve the problems and find adequate solutions, but also is one of the main factors driving membrane technology forward. This review is mainly focused on the organic fouling phenomena of IEMs during ED processes in both food and water treatment industries. It principally presents the main cleaning techniques used in industry or experimented at laboratory scale and the recent strategies of fouling prevention.