Spray drying and gastrointestinal transit can cause substantial losses in probiotic viability, limiting effective delivery in food applications. This study developed a thermophysically guided framework for the rational design of Lactiplantibacillus plantarum microcapsules in three sequential stages. First, Kissinger kinetic analysis of eleven biopolymer candidates (E_a: 95.4–198.4 kJ/mol) combined with pH-dependent solubility profiling provided an empirical screening criterion for the preselection of coating materials; the activation energies are apparent values associated with a composite endothermic event and the glass transition temperature was not measured in this work. Second, a factorial design identified whey protein concentrate (WPC)–gum arabic as the most suitable wall system, yielding a post-drying survival of 97.76 ± 0.75% and showing a significant protein–polysaccharide interaction (p < 0.0001). Third, a D-optimal mixture design optimized a four-component thermoprotectant blend composed of trehalose (29.7%), glycerol (25.7%), fructooligosaccharides (19.8%), and inulin (24.8%). The fitted model explained 91.9% of the response variability (R² = 0.919), and the optimized blend limited viability loss during thermal exposure at 92 °C for 3–8 min, consistent with complementary protective effects involving vitrification and membrane stabilization. The optimized system yielded 2.4 × 10¹¹ CFU/g after spray drying, a water activity of 0.23, and a Carr Index of 18.5%. Under simulated gastrointestinal digestion (INFOGEST 2.0), thermoprotectant-loaded microcapsules retained 1.5 × 10⁷ CFU/mL of digesta after the gastric phase and delivered 1.2 × 10⁸ CFU/mL of digesta to the intestinal phase, four to five orders of magnitude above unprotected microcapsules (1.0 × 10³ CFU/mL of digesta). Overall, these results support a transferable formulation strategy that combines thermophysical screening with experimental design to develop probiotic ingredients with improved thermal stability for food applications.