The effects of simulated processing (pH adjustment and thermal treatment) on the antioxidant capacity and in vitro protein digestion of fruit juice-milk beverage (FJMB) models consisting of whey protein (WP), and chlorogenic acid (CHA) or catechin (CAT) were investigated. Results indicated that CAT was more susceptible to processing than CHA, and showed a significant (p < 0.05) decrease in ABTS and FRAP after sterilization (121 °C/10 min) and pH adjustment to 6.8. WP addition had different effects (none, masking, synergetic effect) on the antioxidant activity of FJMB. Pasteurization (63 °C/30 min) and pH adjustment (pH 3.7 or pH 6.8) had either non-significant or slight effects on FJMB’s antioxidant capacity, while sterilization significantly (p < 0.05) increased or decreased its ABTS and FRAP depending on the different models. In vitro digestion of WP in FJMB was obviously (p < 0.05) inhibited by phenolics to varying degrees, and little influenced (p > 0.05) by pasteurization, whereas sterilization initially accelerated WP digestion but did not change its overall digestibility.