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The aqueous anthocyanin-rich extract derived from black rice (Oryza sativa L.) was encapsulated by freeze drying using milk proteins and peptides as coating materials. The molecular modelling approach indicated that all major casein fractions and whey proteins were able to bind at least one anthocyanin molecule. The hydrophobic interactions and hydrogen bonding across the interfaces appeared to be mainly responsible for the stabilizations of the complexes formed between the coating material and bioactive compounds. Two dark purple colored powders, differentiated by the ratio of the encapsulation materials used, rich in phytochemicals were obtained, with an encapsulation efficiency of up to 99%. The powders were tested for antioxidant activity, cytocompatibility, and thermal stability. The morphological structure of the powders highlighted the presence of encapsulated anthocyanins. Both powders showed a remarkable antioxidant activity of about 46 mM Trolox/g D.W., and cytocompatibility on the L929 fibroblast culture. At certain concentrations, both powders stimulated cell proliferation. The powders showed a good thermal stability between 75 and 100 °C for 15 min. The powders were tested in a food model system and checked for stability of phytochemicals during storage. The added value of the powders was demonstrated throughout the antioxidant activity, which remained unchanged during storage.