The presence of membrane fouling is the main drawback in membrane processes, and it is related to the premature use and high cost for the replacement of membranes. Polyphenols in cranberry juice are associated with ion-exchange membrane fouling, and it results in a loss of these beneficial compounds in the juice when treated by membrane processes such as electrodialysis. In the present work, four heterogeneous or pseudohomogeneous cation-exchange membranes (CSE-fg, MK-40, CEM Type-II, and CJMC-5), different in terms of the polymer matrix (aromatic, aliphatic), exchange capacity, size, and location of meso and macropores, were studied to understand the impact of the membrane structure and physico-chemical properties on adsorption and desorption of phenolic compounds (anthocyanins and proanthocyanidins) from cranberry juice. It appeared from these results that MK-40, CEM Type-II, and CSE-fg were more prone to fouling due to their high ion-exchange capacity, their thickness, and the presence of meso and macropores in their structure. Indeed, electrostatic interactions occurred between fixed groups of membranes and polyphenolic ions. Desorption of the entire membrane and cryogenic grinding with pH adjusted to 10 allowed a better recovery of anthocyanins and proanthocyanidins (PACs), respectively, since hydroxide ions competed with polyphenols and membrane that induced desorption of polyphenols. In the future, this new knowledge will become the basis for a more sensible choice of membranes and for the development of protocols for extending their life cycle.