Objectives: This study investigates the biological activities of microencapsulated anthocyanins extracted from two Andean ancestral edible plants, Solanum tuberosum, and Zea mays, with a focus on their potential applications in functional foods and therapeutics. The primary objective was to evaluate their antioxidant, antimicrobial, and cytotoxic properties alongside structural and functional analyses of the microencapsulation process. Methods: Anthocyanins were extracted and microencapsulated using maltodextrin as a carrier. Fourier-transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) were employed to analyze the stability and structure of the microencapsulated particles. The antioxidant, antimicrobial, and cytotoxic activities of the microencapsulated were assessed through established assays. Results:S. tuberosum exhibited superior antioxidant capacity and potent anticancer activity against HepG2 and THJ29T cell lines, while Z. mays demonstrated significant antimicrobial efficacy against multidrug-resistant bacterial strains and biofilm-forming pathogens. Fourier-transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) confirmed the stabilization of anthocyanins within a maltodextrin matrix, enhancing their bioavailability and application potential. Conclusions: These results highlight the versatility of microencapsulated anthocyanins as bioactive agents for industrial and therapeutic applications. Future studies should explore in vivo validation and synergistic formulations to optimize their efficacy and broaden their use in nutraceutical and pharmaceutical fields.