Membranes, more particularly ion-exchange membranes (IEMs), are vulnerable to fouling by peptides and amino acids present in protein hydrolysate. In this context, IEM and ultrafiltration membranes (UFMs) staked in an electrodialysis with filtration membrane (EDFM) system were characterized during and after 6 successive peptide fractionations. The peptide concentration in the recovery compartment decreased by more than 22% and 32% for fifth and sixth batches, respectively. In addition, analysis of total nitrogen content of used membranes and FTIR confirmed that AEM and both cation-exchange membranes (CEMs) were fouled by peptides and/or free amino acids. Consequently, their electrical conductivity, IEC and water content decreased. In addition to the fouling, the cathode (diluate) side of AEM, where the dissociation of water molecules occurs, was deteriorated radically, possibly due to chemical reactions with OH- ions produced. Consequently, the surface roughness of both IEMs was found to increase considerably. The IEM fouling noticed in the present study was never observed before in an EDFM treatment. This fouling would be mainly due to the presence of amino acids residues (100% free) in the SCBH, and able to migrate through the AEM (Phe) and the CEM (Arg and Lys). (C) 2015 Elsevier B.V. All rights reserved.