The aim of the study was to design microcapsules with a core of blueberry fruit extracts (Vaccinium myrtillus L.) using the ionotropic gelation method and then assess the effect of the type of extracts used and the combination of polymers on the profile of phenolic compounds, their in vitro bioavailability, stability during storage, as well as their antioxidant characteristics and cytotoxic activity against colon cancer cells while assessing biocompatibility against normal colon epithelial cells. Encapsulation efficiency (EE), ranging from 8.79 to 74.55%, significantly depended on the extract used and the type of carrier. It was shown that the addition of pectin (Pect) and whey protein isolate (WPI) to alginate (Alg) improved the efficiency of the encapsulation process. For this version of microcapsules, the highest antioxidant activity, phenolic compound content and their stability during storage were also demonstrated. The estimated content of phenolic compounds ranged from 0.48 to 40.07 mg/g, and the dominant compound was cyanidin 3-O-glucoside. In turn, the highest bioavailability of these compounds and the highest cytotoxic activity against cancer cells were characterized by microcapsules with Alg and WPI. Nevertheless, good biocompatibility with normal colon epithelial cells was demonstrated for all versions of microcapsules. The obtained data indicate that the tested variants of microcapsules protect the bioactive compounds of blueberry fruit extracts, which translates into maintaining their health-promoting properties.