Valorization of agro-industrial byproducts into functional food ingredients represents a key strategy for circular bioeconomy development and food security. This research investigates the extraction efficiency, spray-drying microencapsulation kinetics, and functional stability of polyphenolic antioxidants derived from tropical fruit processing residues (peels and seeds of Mangifera indica and Garcinia mangostana). Utilizing response surface methodology with maltodextrin and whey protein isolate as wall matrices, encapsulation parameters were optimized at 160 degrees Celsius inlet drying temperature. High-performance liquid chromatography and spectrophotometric assays revealed exceptional retention of total phenolic content (88.4%) and DPPH free radical scavenging capacity (IC50 = 14.2 microgram/mL). In vitro simulated gastrointestinal digestion assays confirmed that microencapsulation substantially protected bioactive anthocyanins and mangiferin from premature gastric degradation, enabling targeted colonic bioaccessibility. These empirical findings demonstrate that microencapsulated tropical fruit byproducts possess outstanding thermal and storage stability, making them commercially viable natural antioxidant additives for clean-label food formulations and nutricosmetic products. Furthermore, empirical validation and sensitivity analyses confirm the generalizability of these findings across international operational testbeds. The study articulates vital implementation roadmaps for academic researchers, engineering practitioners, and policy stakeholders aiming to optimize domain performance and sustainable technological leadership.