The design of functional foods has grown recently as an answer to rising consumers' concerns and demands for natural, nutritional and healthy food products. Nanoencapsulation is a technique based on enclosing a bioactive compound (BAC) in liquid, solid or gaseous states within a matrix or inert material for preserving the coated substance (food or flavor molecules/ingredients). Nanoencapsulation can improve stability of BACs, improving the regulation of their release at physiologically active sites. Regarding materials for food and nutraceutical applications, the most used are carbohydrate-, protein- or lipid-based alternatives such as chitosan, peptide-chitosan and β-lactoglobulin nanoparticles (NPs) or emulsion biopolymer complexes. On the other hand, the main BACs used in foods for health promoting, including antioxidants, antimicrobials, vitamins, probiotics and prebiotics and others (minerals, enzymes and flavoring compounds). Nanotechnology can also play notable role in the development of programmable food, an original futuristic concept promising the consumers to obtain high quality food of desired nutritive and sensory characteristics.