The aim of this research was to evaluate the influence of in vitro gastrointestinal digestion on the stability and bio-accessibility of phenolic compounds and carotenoids, as well as on the antioxidant activity in strawberry and peach enriched yoghurt. The radical scavenging capacity of strawberry and peach yoghurt was 480 and 550% higher, respectively, at the level of the intestine than in fruit yoghurt not subjected to digestion. In strawberry the amount of bio-accessible anthocyanins increased during gastric digestion and the transition to the intestinal compartment produced a decrease in all the analyzed classes of polyphenols, being more pronounced in pelargonidin-3-glucoside (65%) and pelargonidin-3-rutinoside (58%). In peach the (+)-catechin content strongly decreased (80%), and neochlorogenic, chlorogenic acid, rutin and the carotenoid zeaxanthin decreased at lower levels, between 32-45%, while β-carotene was rather stable under gastric conditions (increased by 12%) during intestinal digestion. Despite the decrease in the concentration of these bioactive compounds after being subjected to in vitro gastrointestinal digestion, results suggest that fruit yoghurt is an important source of bio-accessible polyphenols and carotenoids and that despite some losses induced by digestion conditions, it still releases relevant amounts at the level of the intestine to be absorbed and to promote health benefits.