Background: The increasing prevalence of plant-based dietary preferences, driven by lactose intolerance, allergies, and adherence to vegan diets, has necessitated the exploration of alternative food matrices for probiotic delivery. Objectives: This study aimed to evaluate the effects of whey protein isolate, pea protein isolate, and soy protein isolate on the viability of L. casei and L. johnsonii during simulated in vitro gastrointestinal digestion. Furthermore, the study investigated the impact of two distinct matrices—cow’s milk and an oat-based beverage—on the survival of these probiotic strains. Fermented products were prepared using cow’s milk and an oat-based beverage as matrices, with simulated digestion performed following a seven-day storage period at 5 °C. The in vitro digestion model encompassed oral, gastric, and small intestinal phases, with probiotic viability assessed using the plate-deep method at each stage. Methods: Before digestion, L. casei exhibited higher populations than L. johnsonii in both matrices. Including 3% soy and pea protein, isolates promoted the growth of L. casei in both fermented milk and oat beverages. However, a marked reduction in probiotic viability was observed during the gastric phase, with L. casei counts decreasing by 6.4–7.8 log cfu g−1 in fermented milk and 3.1–4 log cfu g−1 in oat beverages, while L. johnsonii demonstrated similar reductions. Conclusion: These findings underscore the protective role of dairy components on probiotic viability, while the oat-based matrix exhibited a reduced capacity for sustaining probiotic populations throughout digestion. Future research should focus on optimizing plant-based matrices to enhance probiotic stability during gastrointestinal transit.