The inulin is known as a prebiotic carbohydrate with beneficial health properties in addition to its technological properties as a texture modifier and stabilizer of food products. Despite that, a little is known about the influence of the degree of inulin polymerization during gastrointestinal digestion. Then, the objective of this study was to evaluate if the degree of inulin polymerization influences the bioaccessibility of bioactive compounds during in vitro gastrointestinal digestion of a functional soursop (Annona muricata) whey beverage. Therefore, two beverages were manufactured using inulin with different degrees of polymerization (DP), inulin GR (DP ≥ 10) and inulin HP (DP ≥ 23). To evaluate the effects of the inulin DP during in vitro digestion on the microstructure, total phenolic content, antioxidant activity, sugars and fructo-oligosaccharides content, the samples produced with inulin GR and HP were submitted to a simulated gastric and intestinal digestion and the digesta samples were analyzed after each digestion step (undigested, gastric digested and intestinal digested). Overall, the whey beverages produced with inulin of different degrees of polymerization originated products and respective digesta with different characteristics related to the microstructure and the sugars and fructo-oligosaccharides. Despite the different behavior during in vitro digestion, after intestinal digestion, where the compounds could be absorbed, the bioaccessibility of the bioactive compounds and antioxidant activity of both digesta were similar, suggesting the possibility of production of a soursop whey beverage with inulin of different DP without influencing its functional quality.