Probiotics die over time during processing, storage and digestion, resulting in reduced health benefits to the consumer. Microencapsulation of microorganisms is an effective way to improve probiotic viability by restricting cell exposure to extreme conditions through the gastrointestinal tract until release in the colon. In this work, appearance and survival of encapsulated probiotic species from two genera was explored. Lactococcus lactis and Bifidobacterium longum were suspended in calcium alginate microbeads by spraying droplets of alginate-probiotic mixture into calcium chloride solution. This produced uniformly shaped transparent microbeads with high encapsulation yield. Encapsulating Lactococcus lactis extended viability during dry room temperature storage. Encapsulating Bifidobacterium longum revealed high variation between eight different strains from subspecies longum and infantis. Coating alginate particles with chitosan did not improve viability and, viability of free and encapsulated bifidobacteria decreased when exposed to simulated gastric and intestinal conditions. Data from these studies suggest microencapsulating probiotic cells is an invaluable process to extending cell viability. Future research should optimize current formulations to improve encapsulation yield and cell survival during processing, storage, and gastrointestinal transit.