The need for encapsulation processes in compounds such as procyanidins (PCs) is related to their functional stability, which may limit their application in functional foods. The aim of this study was to evaluate the in vitro digestion of microencapsulated PCs from litchi peel and coffee pulp to determine concentration changes and antioxidant activity. The PCs were extracted, purified, encapsulated, and subjected to in vitro digestion and absorption. Phenolic acids, flavonoids, and PCs were characterized by UPLC-PDA-ESI-QqQ, identifying 27 compounds, including PCs with mean degrees of polymerization (mDP) of 1.2 and 1.7 for lychee and coffee. It was shown that the concentrations of encapsulated PCs were adequately retained during digestion (94.81 ± 4.83 and 90.74 ± 1.77%, lychee and coffee, respectively), with variation in their antioxidant capacity (68.33 ± 2.89 and 77.07 ± 4.59%)
however, they showed better results than in their free form. Additionally, litchi PCs showed a higher absorption rate (100%) than coffee PCs (60%). These results allowed us to determine that encapsulation preserves the properties of the PCs and provides better conservation percentages than other studies, which could be a valuable addition to the functional ingredients market, offering greater value to these by-products.