A previous study on skim milk demonstrated that bipolar-membrane electroacidification (BMEA) is a technology that can be used to produce isoelectric precipitation of casein from milk. However, a deposit, suspected to be calcium hydroxide, was observed on the cation-exchange membrane (CEM) side in contact with the base, Also, the performance of the process decreased as well as the lifetime of the membrane. The aim of the present study was therefore to evaluate two types of CEM with different permselectivities in terms of electrodialysis efficiency and membrane parameters, BMEA allowed the separation of high purity bovine mill, casein (about 97% protein), and the permselectivity of both membranes tested does not influence the purity of the isolates produced. However, the migration of cations through the cationic membrane was found to be influenced by the permselectivity leading to isolates with different ash contents. The CSV(TM) membrane slowed down the migration of cations in comparison with CMX(TM) membranes. The membrane fouling of cation-exchange membrane was identified as precipitating calcium and magnesium hydroxides. Moreover, the fouling formed at the outer layer surface of the CEM was demonstrated to be reversible for both membranes while the fouling of the CSV(TM) membrane inner layer was irreversible.