The study examined the effect of fortification of bean paste with onion skin phenolics. The antioxidant potential and in vitro digestibility of nutrients in the light of phenolic-food matrix interactions were studied. Bean paste was supplemented with onion skin extracts in the range of 5-50 mg of phenolics per 100 g of bean (C, O5-O50). Fortification increased the phenolic level and antioxidant activity of bean paste; however, the experimental values, in most cases, were significantly lower than those predicted. The digestive tract acted as an effective extractor of phenolics from the functional products but, surprisingly, the amounts of introduced phenolics had no significant effect on its determined levels. Additionally, after in vitro intestinal digestion a significant increase in the ability to quench free radicals was only observed in samples enriched with the highest amounts of phenolics (O50). After gastric and intestinal stages of digestion no significant effect of fortification on the albumin digestibility was observed. Contrarily, digestibility of globulins had decreased from 70% (C) up to 55% (O50) after gastric digestion and from 93% (C) up to 80% (O50) after intestinal digestion. These results were confirmed by SDS-PAGE analysis, which indicates the presence of indigestible complexes after supplementation with phenolics. Moreover, a significant decrease in starch digestibility from 43% (C) to 21% (O50) was found. In conclusion, fortification improves the health-promoting properties of bean paste; however, the interactions of phenolics with the food matrix play an important role in the creation of the nutraceutical and nutritional quality of products.