Brazilian native fruits are reported to be promising sources of bioactive compounds; however their bioactivity depends on their stability along the digestive process. This study evaluated the α-glucosidase inhibition, antioxidant activity and total phenolic content (TPC) stability of araçá, butiá and pitanga fruit extracts using an in vitro digestion model. Additionally, the individual phenolic compound recovery of the most stable and active extract was evaluated by HPLC-DAD-ESI-MS/MS. Overall, the antioxidant activity of all extracts decreased along the process. Araçá fruit extracts, at the end of digestion, showed α-glucosidase inhibition values similar to their non-digested extracts and the highest TPC recovery (28%). Recovery of individual phenolic compounds of red araçá fruit extract revealed a negative impact on the stability of ellagitannins. Araçá fruit extract seems to provide phenolic compounds with α-glucosidase inhibitory properties after the gastrointestinal digestion, indicating their potential to be used in the control of type II diabetes.