Probiotics play a pivotal role to reduce gastrointestinal problems by exerting a drastic effect on various pathogenic microflora of the colon. Lactobacillus reuteri CECT-925 loaded beads were prepared by emulsion containing sodium alginate and sesame seed oil. Encapsulation was done by spraying emulsion into a 0.5% solution of calcium chloride. Microencapsulated probiotics incorporated guava juice was assessed for physicochemical analysis at the 15-day interval for 60 days. The juice was tested for probiotics viability, titratable acidity, pH, total soluble solids and organoleptic properties. In the control sample, viable counts of encapsulated probiotics were reduced from 7.68 to 1.96 log10 CFU/ml while in T₁, T₂ and T₃ the initial numbers 7.39, 7.7 and 7.87 were reduced to 5.97, 6.87 and 6.02 log10 CFU/ml respectively at the termination of the storage period. However, pH and sensory scores decreased while total soluble solids and titratable acidity increased. Results indicated that microencapsulation by sodium alginate in combination with sesame oil retained the viability of Lactobacillus reuteri > 90% in guava juice. The acceptability of the product was 82.04% till the end of the storage period.