This study investigated the viability and resilience of free and encapsulated probiotic bacteria (Lactobacillus plantarum and Lactobacillus casei) in commercial apple and tomato juices during refrigerated storage and simulated gastrointestinal digestion. Individual probiotic species were encapsulated via freeze-drying and added to apple and tomato juices at 1% concentration. Samples were then stored refrigerated at 4°C for 28 days and analyzed for Lactic Acid Bacteria (LAB) counts, physicochemical properties (colour, pH, titratable acidity, total phenols) on days 1, 14, and 28, and in-vitro digestion and colonic fermentation were performed on days 1 and 21. Results showed the potential of encapsulation to enhance probiotic viability during storage and digestion compared to free probiotics. L. plantarum exhibited superior acid and bile tolerance than L. casei. Prolonged storage in acidic conditions led to a gradual decrease in LAB counts with noticeable variability in physicochemical properties. Total phenols also fluctuated due to microbial utilization, enzymatic degradation and pigment oxidation. Despite the consistently low pH, apple and tomato juices enriched with encapsulated probiotics could be applied effectively as a probiotic carrier matrix for up to 14 days of refrigerated storage. Thus, offering an alternative to traditional dairybased carriers.