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Cornus mas was used in this study as a rich source of health-promoting bioactives. The cornelian cherries were used to extract the polyphenols and anthocyanins. The chromatographic profile of the Cornus mas fruit extract revealed the presence of several anthocyanins, mainly delphinidin, cyanidin and pelargonidin glycosides. The extract was co-microencapsulated with Lactobacillus casei ssp. paracasei in a unique combination of whey protein isolates, inulin and chitosan by freeze-drying, with an encapsulation efficiency of 89.16 ± 1.23% for anthocyanins and 80.33 ± 0.44% for lactic acid bacteria. The pink-red colored powder showed a total anthocyanins content of 19.86 ± 1.18 mg cyanidin-3-glucoside/g dry weight (DW), yielding an antioxidant activity of 54.43 ± 0.73 mMol Trolox/g DW. The viable cells were 9.39 × 10⁹ colony forming units (CFU)/g DW. The confocal microscopy analysis revealed the microencapsulated powder as a complex one, with several large formations containing smaller aggregates, consisting of the lactic acid bacteria cells, the cornelian cherries’ bioactive compounds and the biopolymers. The powder was tested for stability over 90 days, showing a decrease of 50% in anthocyanins and 37% in flavonoids content, with no significant changes in antioxidant activity and CFU. The powder showed a significant inhibitory effect against the α-amylase of 89.72 ± 1.35% and of 24.13 ± 0.01% for α-glucosidase. In vitro digestibility studies showed a significant release of anthocyanins in gastric juice, followed by a decrease in intestinal simulated conditions. The functional properties of the powder were tested by addition into a …