Whey protein concentrate (WPC) and native agave fructans (NAFs) were used in the microencapsulation process of Lactobacillus acidophilus La-14 or Bifidobacterium longum subsp. infantis. Two treatments were carried out: 1. double emulsion-WPC-NAF and 2. WPC-NAF, both treatments were spray dried. Physicochemical, flow, and reconstitution properties, as well as thermal and microstructural stability were evaluated in microcapsules. Encapsulation efficiency after storage (one year, 4 °C) was determined under simulated gastrointestinal tests. The double emulsion-WPC-NAF showed an encapsulation efficiency >76%, whereas this efficiency reached up to 95% in dried microcapsules. Both treatments showed viability of 8 and 9 log CFU/g after storage and in vitro digestion, respectively. Also, the formation of structural WPC-NAF complexes, related to thermal and structural stability, was observed in microcapsules of double emulsion-WPC-NAF. Hence, microcapsules made from double emulsion of WPC-NAF showed greater physicochemical, structural, and microbial stability, suggesting their use as potentially functional food additive.