Tofu whey, a by-product of tofu production, is rich in nutrients such as proteins, minerals, fats, sugars and polyphenols. In a previous work, protein recovery from tofu whey was studied by using a coupled environmental process of ED + EDBM to valorize this by-product. This process allowed protein recovery by reducing the ionic strength of tofu whey during the ED process and acidifying the proteins to their isoelectric point during EDBM. However, membrane fouling was not investigated. The current study focuses on the fouling of membranes at each step of this ED and EDBM process. Despite a reduction in the membrane conductivities and some changes in the mineral composition of the membranes, no scaling was evident after three runs of the process with the same membranes. However, it appeared that the main fouling was due to the presence of isoflavones, the main polyphenols in tofu whey. Indeed, a higher concentration was observed on the AEMs, giving them a yellow coloration, while small amounts were found in the CEMs, and there were no traces on the BPMs. The glycosylated forms of isoflavones were present in higher concentrations than the aglycone forms, probably due to their high amounts of hydroxyl groups, which can interact with the membrane matrices. In addition, the higher concentration of isoflavones on the AEMs seems to be due to a combination of electrostatic interactions, hydrogen bonding, and π–π stacking, whereas only π–π stacking and hydrogen bonds were possible with the CEMs. To the best of our knowledge, this is the first study to investigate the potential fouling of BPMs by polyphenols, report the fouling of IEMs by isoflavones and propose potential interactions.