Acquisition of a healthy lifestyle through diet has driven the food manufacturing industry to produce new food products with high nutritional quality. In this sense, consumption of bioactive compounds has been associated with a decreased risk of suffering chronic diseases. Nonetheless, due to their low solubility in aqueous matrices, high instability in food products during processing and preparation as well as poor bioavailability, the use of such compounds is sometimes limited. Recent advancements in encapsulation and protection of bioactive compounds has opened new possibilities for the development of novel food products. In this direction, the present review is attempting to describe encapsulation achievements, with special attention to nanostructured lipid-based delivery systems, i.e., nanoemulsions, multi-layer emulsions and liposomes. Functionality of bioactive compounds is directly associated with their bioavailability, which in turn is governed by several complex processes, including the passage through the gastrointestinal tract and transport to epithelial cells. Therefore, an overview of recent research on the properties of these nanostructured lipid-based delivery systems with a strong impact on the functionality of bioactive compounds will be also provided. Nanostructured lipid-based delivery systems might be used as a potential option to enhance the solubility, stability, absorption and, ultimately, functionality of bioactive compounds. Several studies have been performed in this line, modifying the composition of the nanostructures, such as the lipid-type or surfactants. Overall, influencing factors and strategies to improve the efficacy of encapsulated bioactive compounds within nanostructures have been successfully identified. This knowledge can be used to design effective targeted nanostructured lipid-based delivery systems for bioactive compounds. However, there is still a lack of information on food interactions, toxicity and long-term consumption of such nanostructures.