Developing stable plant-based probiotic beverages requires innovative formulation strategies. While chickpea aquafaba, a protein-containing by-product, shows promise for the development of functional foods, its specific application in probiotic matrices remains underexplored. This study evaluated a coconut-based probiotic beverage supplemented with aquafaba by monitoring viable cell counts, pH, sugar and organic acid profiles, and antioxidant activity during 30 days of refrigerated storage. A 22 full factorial experimental design was used to investigate the effects of aquafaba and sucrose concentrations on the viability of Lacticaseibacillus casei NRRL B-442. The selected formulation (30% aquafaba and 50 g/L sucrose) achieved the highest viable cell count after fermentation (9.88 ± 0.09 log CFU/mL), compared with 8.40 ± 0.07 log CFU/mL in the control (coconut). During 30 days of refrigerated storage, the formulation R4 maintained probiotic viability above the recommended functional threshold (>7.0 log CFU/mL), reaching 7.40 log CFU/mL at day 30, whereas the control (coconut) declined to 6.77 log CFU/mL. R4 formulation also exhibited a slower decline in pH (4.50 vs. 3.20 in the control (coconut) at day 30) and higher lactate concentration after fermentation (2.04 vs. 0.79 g/L). Carbohydrate profiling revealed sustained sucrose utilization during storage, while the control (coconut) showed early metabolic stabilization. Monte Carlo simulation estimated an 87.9% probability for R4 and 24.8% for the coconut control of meeting the predefined viability criterion of 7.0 log CFU/mL under the modeled storage conditions. R4 beverage maintained viable cell counts above the predefined criterion of 7.0 log CFU/mL throughout storage, unlike the control (coconut). These results emphasize that integrating formulation optimization with predictive microbiology and stochastic modeling is a key component for developing robust probiotic plant-based beverages. This approach provides a complementary framework for evaluating uncertainty in predicted probiotic viability under the evaluated storage conditions.