Probiotics are susceptible to moisture migration, oxygen exposure, and temperature fluctuations during ambient storage. These stresses can damage cellular structures and reduce viable cell counts, limiting the application of probiotics in products distributed without refrigeration. Encapsulation offers a promising approach to improving storage stability by providing physical barriers, regulating the surrounding microenvironment, and mitigating cellular damage. This review summarizes the major mechanisms of probiotic inactivation during ambient storage. It examines the protective roles of polysaccharide-, protein-, lipid-, and composite-based materials and compares the protective effects, limitations, and industrial applicability of different encapsulation techniques. Key indicators and challenges in evaluating storage stability are also discussed. Current evidence suggests that probiotic stability depends not only on the barrier properties of encapsulation materials but also on intrinsic stress resistance, processing-induced damage, and the physical state of the encapsulating matrix. However, gaps remain between laboratory findings and industrial applications, and inconsistent evaluation methods limit comparisons across studies. Future research should integrate intrinsic stress-resistance enhancement with extrinsic encapsulation strategies, establish standardized and multidimensional evaluation systems, and validate long-term stability in real food matrices under industrially relevant conditions.