Probiotic functionalization of non-dairy beverages has been garnering interest to provide dairy-sensitive populations with greater probiotic product varieties. The addition of probiotics into popularly consumed beverages–carbonated sodas and beers, presents an interesting challenge as the presence of acidic pH, hops-derived compounds, and ethanol have highly deleterious effects. Herein, alginate encapsulation was proposed to improve probiotics viability within sodas and beers. Three probiotics, namely Lacticaseibacillus rhamnosus GG, Escherichia coli Nissle 1917, and Bifidobacterium longum were encapsulated in alginate spheres and exposed to Coca-Cola, 7-Up, Tiger Beer, and Guinness under refrigerated, room temperature and simulated gastric fluid conditions. Results demonstrate that alginate encapsulation significantly improved the viabilities of all three probiotics in various beverages and conditions. Refrigerated storage better preserved probiotic viabilities and reduced the formation of the probiotic metabolic by-product, L-lactate, than at room temperature storage. Findings here could provide beverage manufacturers with a novel way to develop probiotic-sodas and probiotic-beers through encapsulation.