To optimize cranberry juice enrichment, correlation between physicochemical properties of filtration membranes (FM) and anthocyanin migration was investigated during electrodialysis with filtration membranes (EDFM) using redundancy (RDA) and multivariate regression (MRGA) analyses. Six polyether sulfone (PES) and polyvinylidene fluoride (PVDF) membranes with molecular weight cut-offs between 150 and 500 kDa, commercially available at large scale, were characterized in terms of nine physicochemical characteristics and used for EDFM. The highest migration of total anthocyanin was obtained with PVDF 250 kDa, with a global migration rate of 3.5 ± 0.4 g/m2·h. RDA showed that two FM properties (mesopore porosity and hydrophilic porosity) were significantly negatively correlated to the anthocyanin's migration and explained 67.4% of their total variation in migration. Predictive MRGA models were also developed for each anthocyanin based on these significant FM properties. A combination of intermolecular interactions may lead to binding in a cooperative and synergistic mode and hinder the anthocyanin migration.