Five yeast strains (four wild Saccharomyces cerevisiae strains and a collection strain-S. cerevisiae var. boulardii) were encapsulated in alginate beads. Encapsulation yield was at least 60% (100% for some strains) and yeasts survived in beads for 30 days at 4 °C, although the viability was strongly affected during storage at 25 °C (3 log reduction after 7 days). The kinetic of cell release was studied under static and dynamic conditions, but the results suggest that, after 48 h, beads contained a high number of yeasts. Thus, their use is advisable as re-usable carriers of starter cultures or as a vehicle of probiotics into the gut. Finally, some functional properties (biofilm formation, hydrophobicity, auto-aggregation, survival during the transit into the gut) were evaluated on yeasts released by beads to assess if microencapsulation could negatively affect these traits. The results showed that yeasts’ entrapment in beads did not affect probiotic properties.