The study evaluated lentil and adzuki bean sprouts as carriers for S. cerevisiae var. boulardii. The highest count of yeast was found in the adzuki bean and lentil sprouts obtained from seeds soaked in inoculum and cultivated at 30 °C–1.03 × 107 CFU/g and 2.5 × 107 CFU/g, respectively. Probiotic yeast effectively survived during digestion in vitro. There was no statistically significant effect of the probiotic on mesophilic bacterial counts; however, the sprouts enriched with S. boulardii were characterized by lower mold counts (by about 99% in the lentil and adzuki bean preparations) and coliform counts (by about 92% and 71% in the lentil and adzuki bean, respectively). In the adzuki bean the highest antiradical properties were determined for the extracts obtained after gastro-intestinal digestion; however, except a potentially bioaccessible fraction, there were no significant differences between the probiotic-rich and control sprouts. Co–culture of adzuki bean sprouts and S. cerevisiae var. boulardii significantly decreased protein content in the fresh (45%) and stored sprouts (54%). Starch content and its digestibility, regardless the type of sprouts, were higher in the control sprouts. Legumes sprouts enriched with S. cerevisiae var. boulardii are a new functional food product characterized by safety and high nutritional and pro-health properties.