<p>Blackberries (<i>Rubus fruticosus</i>) are a rich source of phenolics and anthocyanins, which are associated with antioxidant activity and health benefits after consumption. The aim of this research was to evaluate proteolysis, glycolysis, and physicochemical properties of five microcapsule formulations of blackberry juice during in vitro gastrointestinal digestion, assessing the effectiveness of microencapsulation to preserve and target delivery of bioactive compounds. The microcapsules (1.47–12.1&#xa0;µm) sowed dents, crevices, agglomerates, and rough surfaces, although some of them presented smooth surfaces. Results of in vitro digestion showed that the juice encapsulated in a blend of whey protein isolate (WPI) and maltodextrin (MD) had the highest proteolysis value in the intestinal phase, reaching 52.99%. The major glycolysis was registered in the oral phase, with the microcapsules containing maltodextrin reaching the highest values (~ 265%). All microcapsule formulations effectively protected the bioactive compounds of the juice until they reached the intestine, where their bioactivity is most beneficial. A higher total phenolic content was observed in the juice and microcapsules compared to the total monomeric anthocyanins, although the values of both parameters changed in the oral, gastric, and intestinal phases. Encapsulation of blackberry juice using WPI microcapsules retained the highest phenolic compound content after the spray drying process and during all digestion phases compared to formulations blended with MD or Arabic gum (AG). Results indicate that this encapsulation technology has a high potential to protect and target delivery of bioactive compounds in juices during digestion.</p>