The global coffee industry, a cornerstone of economic and cultural life, faces evolving consumer demands for a holistic experience integrating taste, health benefits, and convenience. This shift necessitates innovative product development, ensuring consumer satisfaction and stringent food safety standards. This study introduces instant cold brew coffee in powder form as a significant technological advancement. This format preserves fresh coffee's sensory quality while substantially improving product stability and shelf life, directly addressing food quality. It also inherently mitigates microbial risk, simplifies logistics, and reduces supply chain costs—all critical for enhancing food safety and efficiency. Driven by increasing gut health awareness, we explored integrating lactic acid bacteria (LAB) into this innovative coffee. Research meticulously investigated the stress adaptation of five LAB strains under various sublethal conditions; notably, Lactobacillus casei showed superior resilience to heat and cold stress, while Lactobacillus acidophilus demonstrated stronger tolerance to acidic environments and bile salts. To simulate industrial drying, probiotic strains underwent thermal challenges, revealing that acid adaptation significantly enhanced L. acidophilus TISTR 1338's heat tolerance. A novel encapsulation method, utilizing rice bran-derived prebiotics, pectin, and resistant starch via crosslinking and freeze-drying, was developed to enhance probiotic viability under harsh processing and storage. This innovation achieved the highest encapsulation efficiency, ensuring encapsulated probiotics retained a viable count of 5 log CFU/g after in vitro digestion, meeting functional food thresholds. Ultimately, this innovation enables synbiotic cold brew coffee that delivers tangible health benefits, setting new benchmarks for modern food safety and quality. By transforming a perishable beverage into a stable, safe, and functional powdered product, this research marks a significant advancement in functional beverage technology and probiotic delivery systems, benefiting producers and consumers alike through innovation and a strong commitment to quality.