The probiotic yeast, Saccharomyces cerevisiae boulardii, was microencapsulated in a mixture of alginate-inulin-xanthan gum, and its ability to grow in berry juice and survive 4 weeks of storage at 4 °C was determined. Exposure of the yeast in these forms to artificial gastrointestinal conditions was also assessed. Encapsulation significantly enhanced cell viability after fermentation and storage compared with the free yeast (7.59 log10 colony forming units/ml versus 6.98 log10 colony forming units/ml, respectively) and protected it from exposure to a simulated gastrointestinal transit after 4 weeks of storage. Conversely, a dramatic loss of viability was exhibited by free yeast after 4 weeks of storage, and viability values closer to zero (0.23 log10 cfu/ml) were found after the simulated gastrointestinal treatment. Microcapsules were capable of absorbing a certain amount of polyphenols and anthocyanins. This work, based on use of microencapsulated probiotic yeasts, might represent the starting point for the development of new functional foods or functional ingredients. Microcapsules were capable to absorb, from berry juice, a certain amount of anthocyanins which, maintaining their native form after the in vitro gastrointestinal transit, might in vivo therein be transformed into other, simpler molecules, with beneficial effect on microflora and human health too.