The effect of high-intensity pulsed electric fields (HIPEF) or thermal processes and refrigerated storage on water-soluble vitamins and antioxidant capacity of beverages containing fruit juices and whole (FJ-WM) or skim milk (FJ-SM) was assessed. Peroxidase (POD) and lipoxygenase (LOX) inactivation as well as color changes were also studied. High vitamin C retention was observed in HIPEF and thermally treated beverages, but a significant depletion of the vitamin during storage occurred, which was correlated with antioxidant capacity. HIPEF treatment did not affect the concentration of group B vitamins, which also remained constant over time, but thermally treated beverages showed lower riboflavin (vitamin B2) concentration. With regard to enzyme activity, thermal processing was more effective than HIPEF on POD and LOX inactivation. The color of the beverages was maintained after HIPEF processing and during storage. Consequently, HIPEF processing could be a feasible technology to attain beverages with fruit juices and milk with high vitamin content and antioxidant potential.