Probiotics play an important role in functional foods, but their viability is often reduced by environmental stresses and storage conditions. This study evaluated the effect of microencapsulation of Limosilactobacillus fermentum 4-17 in an alginate–inulin matrix (0.5–1.5%) on probiotic survival under simulated gastrointestinal conditions and in yogurt. Microcapsules were produced using an emulsion–gelation method and characterized for encapsulation efficiency, structure, and stability. The results showed that incorporating inulin improved encapsulation efficiency and enhanced the structural integrity of the microcapsules. Encapsulated cells exhibited significantly higher survival under gastrointestinal conditions and during refrigerated yogurt storage compared to free cells. In addition, the inclusion of inulin contributed to improved physicochemical properties of yogurt, including viscosity, water-holding capacity, and texture stability. Overall, the alginate–inulin system effectively enhanced probiotic viability and yogurt quality, demonstrating its potential as a promising synbiotic approach for developing stable functional dairy products.

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