This study aimed to examine the bioaccessibility of fruit polyphenols and the effect of β-glucan on polyphenol bioaccessibility. An in vitro simulation of peel and flesh digestion of fruits of traditional and commercial apple cultivars (Malus domestica Borkh.) and black elderberry (Sambucus Nigra L.) was performed, without and with the addition of β-glucan. Experimental data (amount of polyphenols released during digestion (ct) as a function of time (t)) were analyzed by kinetic equations. The effect of polyphenols on α-amylase and α-glucosidase activity was also investigated. Polyphenol classes of peel and flesh of apples and black elderberries were found as potential inhibitors of α-amylase and α-glucosidase. Polyphenols become available for absorption in the digestive system in amounts that are significantly lower than those present in fruit before digestion. After digestion in the mouth, the amount of total polyphenols released in the stomach showed a significant increase and decreased significantly after digestion in the small intestine. Polyphenolic classes showed different behaviours during simulated digestion. After the oral phase, the amount of all polyphenolic classes showed a significant increase after gastric digestion. After small intestine digestion anthocyanins and flavan-3-ols completely disappeared or showed a significant reduction, phenolic acids and dihydrocalcones showed a significant reduction, while the amount of flavonols was similar. β-glucan reduced the amount of polyphenols released, which was statistically significant in some cases. First and second order equations were modified and adjusted for the characteristic release and degradation of polyphenols during simulated digestion. Nonlinear regression of ct data as a function of t modified by the first order equation showed a smaller standard error compared to the second or zero order reactions. Simulated digestion of polyphenolic classes in the stomach and small intestine follows first-order kinetics with a half-reaction time within 10 minutes of the process duration. β-glucan plays a potentially important role in the bioaccessibility of polyphenols and the amount that reaches the lower parts of the digestive system which is important for the various positive bioactivities of polyphenols. The modified kinetic equations used for the first time in this paper can be applied in further studies of polyphenol bioaccessibility.