The application of probiotics is limited by the loss of survival due to food processing, storage, and gastrointestinal tract. Encapsulation is a key technology for overcoming these challenges. The review focuses on the latest progress in probiotic encapsulation since 2020, especially precision engineering on microbial surfaces and microbial-mediated role. Currently, the encapsulation materials include polysaccharides and proteins, followed by lipids, which is a traditional mainstream trend, while novel plant extracts and polyphenols are on the rise. Other natural materials and processing by-products are also involved. The encapsulation types are divided into rough multicellular encapsulation, precise single-cell encapsulation, and microbial-mediated encapsulation. Recent emerging techniques include cryomilling, 3D printing, spray-drying with a three-fluid coaxial nozzle, and microfluidic. Encapsulated probiotics applied in food is an upward trend in which “classic probiotic foods” (yogurt, cheese, butter, chocolate, etc.) are dominated, supplemented by “novel probiotic foods” (tea, peanut butter, and various dry-based foods). Future efforts mainly include the effect of novel encapsulation materials on probiotics in the gut, encapsulation strategy oriented by microbial enthusiasm and precise encapsulation, development of novel techniques that consider both cost and efficiency, and co-encapsulation of multiple strains. In conclusion, encapsulation provides a strong impetus for the food application of probiotics.