In the last years, demand for functional products containing both prebiotics and probiotics (known as synbiotic) has increased, which stimulated their incorporation into other food matrices than milk-based ones. Synbiotics improve gut functionality as well as respond to the increasing demand of consumers who have become aware of the health benefits of a proper diet. The most important criterion for preserving consumer acceptance in such products is maintaining the minimum viability and activity of probiotics from the beginning of production to the end of shelf-life. For their viability, fixation and multiplying within the host, several solutions have been proposed including the fortification with prebiotics and microencapsulation of prebiotics along with probiotics. The challenge of microencapsulation is to protect the probiotic cells in foods that are not usually considered their vehicle, such as fruit matrices. It is generally known that different prebiotics may exert different degrees of protection on the entrapped bacteria cells. For food products, such as fruit beverages, few works exist that investigate the functionality of synbiotic microcapsules in protecting the survivability of probiotic cells during processing and storage. This article provides an overview of this novel trend based on a review of relevant literature. The article summarizes the synbiotic concept, challenges for synbiotic formulation in fruit beverages, and future perspectives.