Isotonic drinks, fortified with microencapsulated maltodextrin and inulin isoflavone extract, were evaluated by organoleptic assessment and color measurement on the CIE L * a * b scale, then they were subjected to in vitro digestion. Changes of concentrations of isoflavones released during digestion of drinks and their ability to neutralize free radicals (ABTS) were determined. The effect of microencapsulation and storage on isoflavone content in isotonic drinks was also evaluated. In the organoleptic evaluation, beverages without additives and beverages fortified with microencapsulated extract were evaluated as better than a beverage with pure extract. Microencapsulation largely eliminated the unpleasant taste and odor of isoflavones and masked their color. Before digestion, isotonic drinks contained 29.07–43.17 μg of isoflavones in 1 ml. Microencapsulated isoflavones were released gradually during simulated digestion. The highest recovery of these compounds was observed for glycoside and malonylate derivatives of daidzein. Daidzin and genistin with encapsulation showed bioavailability of 0.02%–0.07%. The use of inulin as a carrier increased the stability of microcapsules during the storage of isotonic beverages. Microencapsulated of isoflavones from soybeans can increase the health benefits of conventional beverages available on the market.