The objective of this work was to evaluate the potential of whey protein concentrate (WPC), native agave fructans (NAF), and their mixture (WPC-NAF, 1:1 w/w) as wall materials and evaluate the physicochemical properties and stability of encapsulatedEnterococcus faeciumduring the spray drying, storage, and passage through the simulated gastrointestinal tests. The encapsulated microorganisms with WPC-NAF by spray drying showed greater viability (9.26 log CFU/g) and a higher microencapsulation yield (88.43%). They also had a smaller reduction in the cell count (0.61 log cycles), while the microcapsules produced with NAF had the greatest reduction in viability during the simulated gastrointestinal tests. Similarly, probiotics encapsulated with WPC-NAF revealed a higher survival rate (> 8 log CFU/g) when stored at a water activity of 0.328. The thermal analysis showed that the addition of NAF to the WPC produced a slight shift in the Tg towards temperatures higher than that shown by NAF. Therefore, this study provides evidence that the spray drying process was appropriate to encapsulate the probiotic strainEnterococcus faeciumand that the mixture WPC-NAF protected it from adverse drying conditions and improved the viability ofEnterococcus faeciumduring storage and simulated gastrointestinal tests, demonstrating that the combination of NAF and WPC as encapsulating material is adequate in the production of more stable microcapsules with potential application in various foods.