AbstractIn the present study, three probiotic strains viz. Bifidobacterim bifidum, Lactobacillus casei, and Lactobacillus plantarum were encapsulated in resistant starch derived from Indian horse chestnut (HRS) and rice (RRS) by using freeze drying and emulsification techniques. Encapsulation yield for probiotics was found to be in the range of 71.9%–73.3% and 70.2.2%–73.4% using emulsification and freeze drying techniques. ATR‐FTIR spectral analysis of all the microcapsules reveals peaks in the range of 1332–1371 cm−1 and 2910–2925 cm−1 confirming the presence of encapsulated probiotics. Scanning electron microscopy (SEM) shows granules with size ranging from 4 to 25 µm having different shapes. Cells encapsulated via emulsification show significantly better survivability during storage for a period of 3 months. Moreover, the survival rate of all the three microencapsulated probiotic cells remains comparably better under simulated gastrointestinal conditions than the free cells with minimal difference between the two techniques of encapsulation.