Probiotics are live microorganisms that confer a number of health benefits when consumed in adequate amounts, mostly due to improvement of intestinal microflora. Bacterial strains from the genera Lactobacillus, Bifidobacterium, and Bacillus have been widely studied and are used to prepare ready-to-eat foods. However, the physicochemical stability and bioavailability of these bacteria have represented a challenge for many years, particularly in nonrefrigerated foodstuffs. Microencapsulation (ME) helps to improve the survival of these bacteria because it protects them from harsh conditions, such as high temperature, pH, or salinity, during the preparation of a final food product and its gastrointestinal passage. The most common coating materials used in the ME of probiotics are ionic polysaccharides, microbial exopolysaccharides, and milk proteins, which exhibit different physicochemical features as well as mucoadhesion. Structurally, the survival of improved bacteria depends on the quantity and strength of the functional groups located in the bacterial cell walls, coating materials, and cross-linkers. However, studies addressing the role of these interacting groups and the resulting metabolic impacts are still scarce. The fate of new probiotic-based products for the 21st century depends on the correct selection of the bacterial strain, coating material, preparation technique, and food vehicle, which are all briefly reviewed in this article.