Fruit juices are low-fat, non-alcoholic, lactose-free, and nutritious beverages that are highly desired by consumers. However, fruit juices undergo microbial, enzymatic, and chemical deterioration, which shortens their shelf-life. The demand for healthy fresh fruit juice has encouraged the use of natural agents (such as antimicrobials, vitamins, anti-browning agents, and probiotics) for the protection and fortification of freshly squeezed juices. However, the use of these bioactive agents is limited by their low aqueous solubility, and/or physico-chemical instability, especially in acidic food products. Therefore, their incorporation into encapsulation systems to improve their stability and activity has been considered. This is a review of the literature on the characteristics and efficiency of delivery systems that can be used to load and deliver natural agents designed to be used in fruit juices.