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Two multi-functional powders, in terms of anthocyanins from black rice (Oryza sativa L.) and lactic acid bacteria (Lactobacillus paracasei, L. casei 431^®) were obtained through co-microencapsulation into a biopolymer matrix composed of milk proteins and inulin. Two extracts were obtained using black rice flour as a raw material and hot water and ethanol as solvents. Both powders (called P1 for aqueous extract and P2 for ethanolic extract) proved to be rich sources of valuable bioactives, with microencapsulation efficiency up to 80%, both for anthocyanins and lactic acid bacteria. A higher content of anthocyanins was found in P1, of 102.91 ± 1.83 mg cyanindin-3-O-glucoside (C3G)/g dry weight (DW) when compared with only 27.60 ± 17.36 mg C3G/g DW in P2. The morphological analysis revealed the presence of large, thin, and fragile structures, with different sizes. A different pattern of gastric digestion was observed, with a highly protective effect of the matrix in P1 and a maximum decrease in anthocyanins of approximatively 44% in P2. In intestinal juice, the anthocyanins decreased significantly in P2, reaching a maximum of 97% at the end of digestion; whereas in P1, more than 45% from the initial anthocyanins content remained in the microparticles. Overall, the short-term storage stability test revealed a release of bioactive from P2 and a decrease in P1. The viable cells of lactic acid bacteria after 21 days of storage reached 7 log colony forming units (CFU)/g DW.