In the context of functional foods and beverages, probiotic fruit juices offer a unique opportunity to combine probiotics’ health benefits with fruit juices’ nutritious properties. Since most probiotic food products are dairy products, fruit juices could be a viable alternative to dairy foods. Moreover, the variety of tastes with which these juices can be produced can expand the market for these products to consumers of all ages. Important challenges for the probiotic juice manufacturing industry are stability and sensory properties, which can be altered by probiotics or their metabolites. Any functional food must be healthy but still acceptable to consumers’ tastes. To evaluate the safety of these products, and improve the efficacy of probiotics in fruit juices, innovative technologies have been proposed, such as microencapsulation and the contemporary use of antioxidants.