Agavins are reserve carbohydrates found in agave plants; they present texture-modifying properties and prebiotic capacity by increasing the viability of the intestinal microbiota. Through its hydrolysis, agave syrup (AS) can be obtained and can be used as a sweetener in food matrices. The objective of this work was to evaluate the effect of the variation in the content of agavins and AS on the physical, structural, and viability properties of Saccharomyces boulardii encapsulates incorporated into gelatin gummies. An RSM was used to obtain an optimized formulation of gelatin gummies. The properties of the gel in the gummy were characterized by a texture profile analysis and Aw. The humidity and sugar content were determined. A sucrose gummy was used as a control for the variable ranges. Alginate microcapsules containing S. boulardii were added to the optimized gummy formulation to obtain a synbiotic gummy. The viability of S. boulardii and changes in the structure of the alginate gel of the microcapsules in the synbiotic gummy were evaluated for 24 days by image digital analysis (IDA). The agavins and agave syrup significantly affected the texture properties (<1 N) and the Aw (>0.85). The IDA showed a change in the gel network and an increase in viability by confocal microscopy from day 18. The number of pores in the gel increased, but their size decreased with an increase in the number of S. boulardii cells. Agavins and cells alter the structure of capsules in gummies without affecting their viability.