The formulation of probiotics‐enriched products still remains a challenge for the food industry due to the loss of viability, mainly occurring upon consumption and during storage. To tackle this challenge, the current study investigated the potential of using sodium alginate and inulin (SIN) in combination with various encapsulating materials such as skim milk (SKIM), whey protein concentrate (WPC), soy protein concentrate (SPC), and flaxseed oil (FS) to increase the viability of Lactobacillus casei upon freeze‐drying, under simulated gastrointestinal conditions, during 28 days of storage at 4°C, and in a formulation of millet yogurt. Microstructural properties of microcapsules and co‐microcapsules by SEM, oxidative stability of flaxseed oil in co‐microcapsules, and physicochemical and sensory analysis of the product were performed. The produced microcapsules (SIN‐PRO‐SKIM, SIN‐PRO‐WP, and SIN‐PRO‐SP) and co‐microcapsules (SIN‐PRO‐FS‐SKIM, SIN‐PRO‐FS‐WP, and SIN‐PRO‐FS‐SP) had a high encapsulation rate >90%. Moreover, encapsulated and co‐encapsulated strains exhibited a high in vitro viability accounting for 9.24 log10 CFU/g (SIN‐PRO‐SKIM), 8.96 log10 CFU/g (SIN‐PRO‐WP), and 8.74 log10 CFU/g (SIN‐PRO‐SP) for encapsulated and 10.08 log10 CFU/g (SIN‐PRO‐FS‐SKIM), 10.03 log10 CFU/g (SIN‐PRO‐FS‐WP), and 10.14 log10 CFU/g (SIN‐PRO‐FS‐SP) for co‐encapsulated. Moreover, encapsulated and co‐encapsulated cells showed higher survival upon storage than free cells. Also, the SEM analysis showed spherical particles of 77.92–230.13 µm in size. The physicochemical and sensory analysis revealed an interesting nutritional content in the millet yogurt. The results indicate that the SIN matrix has significant promise as probiotic encapsulating material as it may provide efficient cell protection while also providing considerable physicochemical and nutritional benefits in functional foods.