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The effects of thermal processing and digestive protease on the antioxidant capacity of fruit juice–milk beverage (FJMB) models containing whey protein (WP) and chlorogenic acid or catechin (CAT) under in vitro digestion were investigated. After gastric digestion, the FJMB showed a significant (P < 0.05) increase in ABTS, but little change in ferric reducing antioxidant power (FRAP). Intestinal digestion decreased the FRAP and increased ABTS except in the model containing 0.1% CAT. There were different effects (none, masking, synergistic effect) in the antioxidant activity of the WP and phenolics under digestion. Pasteurisation (63 °C/30 min) had no significant effect on the FJMB's antioxidant capacity, while sterilisation (121 °C/10 min) significantly (P < 0.05) increased, decreased or had no significant effect on ABTS and FRAP under digestion, depending on the model. Pepsin and pancreatin significantly (P < 0.05) decreased the fruit phenolics' ABTS. Ferric reducing antioxidant power was not significantly influenced by pepsin during gastric digestion, but was significantly (P < 0.05) decreased by pancreatin during intestinal digestion. These results would be helpful to improve the efficacy of fruit phenolics in FJMB subjected to thermal processing and to maintain the health benefits of this kind of functional products in the food industry.