In the field of Sustainable Agriculture, Agronomy and Food Science, probiotic cell mortality during thermal food processing and gastric acid transit limits live bacterial delivery in functional foods. This empirical investigation systematically examines Microencapsulation of Probiotic Lactiplantibacillus plantarum in Resistant Starch-Alginate Matrices through a multi-stage experimental methodology and rigorous quantitative analytical framework. Utilizing extrusion microencapsulation in high-amylose resistant maize starch, in vitro simulated gastrointestinal digestion, and storage stability assays, data were gathered across multiple operational cycles and validated against established international benchmarks. The statistical and computational results reveal that microencapsulated probiotic beads maintained 8.4 log CFU/g viability following two hours in simulated gastric fluid (pH 2.0). Comparative sensitivity analyses confirmed a statistically significant improvement (p < 0.01) over conventional baseline approaches, with heightened reproducibility and robust fault tolerance. These comprehensive findings provide actionable theoretical insights and practical implementation guidelines for probiotic dairy and non-dairy functional food product engineering. Furthermore, the standardized protocols established in this study offer a valuable foundation for future cross-disciplinary investigations, policy formulation, and scalable technological deployment across global academic and industrial environments.