Cocoa and coffee are natural sources of phenolic compounds, which are degraded during beans processing of both. For this reason, there is an interest in obtaining extracts of these bio compounds. The aim of this study was uncovering the radical scavenging activity (AC) of mixtures of cocoa and coffee extracts, and the bioavailability of their phenolic compounds, resorting to in vitro models: DPPH and ORAC antioxidant methods, and the characterization of the trans-epithelial transport of cocoa and coffee phenolics through Caco-2 cells monolayer model of the intestinal barrier. The cocoa displayed a higher AC than the coffee regarding both DPPH and ORAC assays, while the mixtures increased in parallel with the percentage of cocoa in the blends. The combination index was calculated to set up the type of interaction in the cocoa-coffee mixtures, obtaining that the mixture 25:75 was moderately antagonistic, 50:50 nearly additive, and 75:25 slightly synergistic. The absorption efficiency of the cocoa phenolic compounds was between 87.9%–97.4%, in the coffee compounds was 100%. The mixtures varied according to the proportion of cocoa and coffee. The results obtained allowed concluding that the phenolic compounds present in cocoa and coffee, respectively, are featured by high bioavailability and a valuable antioxidant capacity, while no pattern was found in the mixtures concerning the real benefit of using them combined.