The aim of this study was to extract, protect and increase the bioaccessibility of phenolic compounds extracted from the Chilean Tórtola common bean. For obtaining phenolic compounds, two methods were analyzed, focusing on their extraction and their drying. In the method where ultrasound-assisted extraction and spray drying were used, we obtained a yield five times greater than the conventional method. Thereafter, we evaluated an encapsulation system with two material shells, alginate and Eudragit L-100. The protective capacity of the capsules was verified by determining antioxidant capacity, total phenolic compounds content, as well as biomedical capacities of powder-encapsulated extract. Antithrombotic activity was evaluated as biomedical capacity, observing a 30% reduction in platelet aggregation. Additionally, quality characteristics were assessed using FITR, microscopic confocal, TGA, and hygrometry techniques. TGA analyses demonstrated the thermal protection of the capsule, reducing the degradation of encapsulated phenolic compounds by threefold compared to the non-encapsulated extract. Finally, two in vitro digestion models were used to simulate the physiological digestion. In both models, we observed an increase in TPC bioaccessibility even over 100%. These results would benefit biomedical applications and industrial processing of phenolic compounds extracted from common beans.