Redundancy analysis (RDA) was used to study the effect of eight physicochemical properties of six filtration membranes (PES, PVDF, CF55, S11, S11 + and S11-) on the performance of electrodialysis with filtration membranes (EDFM) in terms of selective peptides migration. The whey hydrolysate anionic and cationic peptides migrations were quantified and identified. PVDF and CF55 were not selective to the contrary of PES, S11, S11 + and S11-. It appeared that at least two properties among zeta potential, pores/surface hydrophilicity, porosity, and roughness were significantly related to the migration of ALPMHIR, IDALNENK, LIVTQTMK, TKIPAVFK, TPEVDDEALEK, TPEVDDEALEKFDK or SLAMAASDISLLDAQSAPLR. These results suggested that the peptides migrations were mainly influenced by the membrane's pore size, and the types of interactions (electrostatic and hydrophilic/hydrophobic) occurring between peptides and membrane. Besides, statistical models for each peptide were also established to predict their specific migration through variety of membranes having different physicochemical properties. To the best of our knowledge, it is the first time that such a method was applied on peptide migration during electrodialysis with filtration membranes.