Limonene, mainly found as a major component in Citrus spp., has been proven to possess a valuable potential as sustainable replacement to synthetic pesticides and food preservatives. This review intends to give a clear overview of the principal emerging applications of limonene in the agri-food industry as antimicrobial, herbicidal and antioxidant agent. To successfully use limonene in a greener agri-food industry, its preservation had become a top concern for manufacturers. In order to elucidate the most efficient and sustainable manner to encapsulate limonene, the different techniques and materials tested up to the present are also reviewed. In general, encapsulation conserves and protects limonene from outside aggressions, but also allows its controlled release as well as enhances its low water solubility, which can be critical for the discussed applications. Other parameters such as scalability, low cost and availability of equipment will need to be taken into account. Further efforts would likely be oriented to the elucidation of encapsulating sustainable systems obtained by cost-efficient elaboration processes, which can deliver effective concentrations of limonene without affecting crops and food products.