Nanotechnology is an emerging field in the food industry that will be important for future industrial production to address rising customer concerns and expectations for natural, nutritious, and healthful food items. People are increasingly motivated to purchase unprocessed food or even high-quality processed foods with minimum chemical additives, highlighting the need to investigate natural alternatives for commercial purposes. Natural compounds are becoming more popular among consumers since they are safer than synthetic chemical additions; however, their most functional compounds are sensitive to the adverse conditions of processing and the digestive tract, impairing their use in food matrices, and industrial-scale applications. Nowadays, nanoencapsulation of natural products can be the most suitable nanotechnology to improve stability, solubility, and bioavailability. The nanostructure can be incorporated into food during production, processing, packaging, and security. Despite the many studies on nanoencapsulation, there is still some misunderstanding about nanoencapsulation systems and preparation techniques. This review aims to categorize different nanoencapsulation techniques (chemical, physicochemical, and physicomechanical), highlight eco-friendly methods, and classify the nanoencapsulation systems as groups (polymer, lipidic and metallic). The current review summarizes recent data on the nanoencapsulation of natural compounds in the food industry that has been published since 2015 until now. Finally, this review presents the challenges and future perspectives on the nanoencapsulation of bioactive compounds in food science.