The oral consumption of probiotic bacteria has become a popular method of improving gut health. However, a large number of potentially probiotic strains are too acid sensitive to survive passage through the gastrointestinal tract, or storage in foods. A popular method of protecting these cells, thereby improving a supplement's efficacy, is by microencapsulation into hydrogels based on the ionic gelation of alginates. The majority of work concerning the use of hydrogels in cell-based therapies involves the study of eukaryotes, and the use of prokaryotic cells, such as probiotics, requires different considerations to be made. Described within this chapter is a description of the development of alginate microencapsulation, its adaptation, and demonstrations of its efficacy in protecting live probiotic cells.