Probiotics must survive in foods and passage through the human mouth, stomach, and small intestine to reach the colon in a viable state and exhibit their beneficial health effects. Probiotic viability can be improved by encapsulating them inside hydrogel-based delivery systems. These systems typically comprise a 3D network of cross-linked polymers that retain large amounts of water within their pores. This study discussed the stability of probiotics and morphology of hydrogel beads after encapsulation, encapsulation efficiency, utilization of natural polymers, and encapsulation mechanisms. Examples of the application of these hydrogel-based delivery systems are then given. These studies show that encapsulation of probiotics in hydrogels can improve their viability, provide favorable conditions in the food matrix, and control their release for efficient colonization in the large intestine. Finally, we highlight areas where future research is required, such as the large-scale production of encapsulated probiotics and the in vivo testing of their efficacy using animal and human studies.