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The aim of this study was to evaluate and compare the efficiency of bovine (CW) and buffalo cheese whey (BCW) as encapsulating agents for the spray-drying (SD) of endogenous Lactobacillus pentosus ML 82 and the reference strain Lactobacillus plantarum ATCC 8014. Their protective features were also tested for resistance to storage (90 days, 25 °C), simulated gastrointestinal tract (GIT) conditions, and for their application in orange juice. Survival rates after SD were approximately 95% in all samples tested, meaning both CW and BCW performed satisfactorily. After 90 days of storage, both species remained above 7 log Colony Forming Units (CFU)/g. However, CW generally enabled higher bacterial viability throughout this period. CW microcapsule characteristics were also more stable, which is indicated by the fact that BCW had higher moist content. Under GIT conditions, encapsulated lactobacilli had higher survival rates than free cells regardless of encapsulating agent. Even so, results indicate that CW and BCW perform better under gastric conditions than intestinal conditions. Regarding their use in orange juice, coating materials were probably dissolved due to low pH, and both free and encapsulated bacteria had similar survival rates. Overall, CW and BCW are suitable encapsulating agents for lactic acid bacteria, as they provided protection during storage and against harmful GIT conditions., Competing Interests: Conflict of interestThe authors declare they have no conflicts of interest., (© King Abdulaziz City for Science and Technology 2020.)