This work describes the applicability of an in vitro digestion model for the evaluation of the digestibility and bioaccessibility of cocoa polyphenols (procyanidins, phenolic acids, and flavones) and for the study of the food matrix effect in relation with the fat content. For this purpose, two cocoa samples, cocoa liquor ( approximately 50% fat content) and cocoa powder ( approximately 15% fat content), were used. The results showed an important increase of the concentration of procyanidin (monomers and dimers), probably due to the hydrolysis of procyanidins with a high degree of polymerization (pentamers to nonamers) submitted to the digestion procedure. In relation to flavones, the concentration of aglycone forms remained almost constant after the digestion steps; in contrast, the concentration of the glycoside forms an increase in the digestion mixtures mainly after the duodenal step, probably as a result of the partial digestion of the dietary fiber present in the cocoa. The higher fat content in the cocoa liquor seemed to have a protective effect, probably related with a better micellarization that favors the stability of polyphenols during digestion.