Defeng Shu, Tianning Zhang, Yajie Dong, Jinlong Xu, Yongkai Yuan
Probiotic viability during processing, storage, and gastrointestinal transit remains a key limitation to probiotic functionality. Although encapsulation is widely used to enhance probiotic survival, most reviews focus on materials and techniques while neglecting strain-specific differences. This review adopts a strain-centered perspective by using Bifidobacterium animalis subsp. lactis BB-12 as a model to systematically reassess encapsulation strategies. By integrating single-strain and co-encapsulation systems, this review elucidates how carrier structure, protection mechanisms, and environmental stresses collectively govern BB-12 stability. In addition, food applications are reinterpreted based on matrix-dependent stress conditions, including acid, osmotic, and oxidative factors. A conceptual “matrix–mechanism–carrier matching” framework is proposed to guide the rational design and selection of encapsulation systems. Overall, this review provides a mechanism-oriented and transferable understanding of probiotic encapsulation, offering practical insights for the design and industrial application of functional foods.