The Electrodialysis with Filtration Membrane (EDFM) system has shown promise in juice enrichment, but further optimization is needed. This study evaluated the effect of processing duration (3 and 6 h) on juice composition, process efficiency, and membrane fouling. Results demonstrated a significant impact of processing time on juice composition, especially anthocyanin and mineral content. Two anthocyanin-depleted juices (−18.94% and −30.70%) and two anthocyanin-enriched juices (26.21% and 44.21%) were produced. Similar energy (1512.13 Wh/g of anthocyanins) was required to migrate equivalent amounts of anthocyanins over both time periods, with no impediment due to fouling observed, although the system’s resistance increased (2.5-fold after 3 h, 3.2-fold after 6 h). Membrane fouling was characterized through conductivity, thickness, ATR-FTIR, SEM-EDX, and foulant identification. Minimal anthocyanin accumulation occurred on cation-exchange membranes (CEM), while anthocyanins and PACs concentrated within the filtering layer of filtration membranes (FM). However, fouling did not increase with longer processing. Structural alterations were noted in anion-exchange membranes (AEMs), suggesting instability under high electric fields. Overall, EDFM effectively enriched cranberry juice with anthocyanins, but further research is necessary to address AEM degradation under limiting current density conditions.