Plastics have been successfully used as packaging materials, but environmental pollution by plastics is inducing a growing interest for alternative, biocompatible plastics. In this context, bionanocomposites are developed for application in the food packaging sector. This article reviews methods for encapsulation of bioactive compounds into nanostructures, which can be further incorporated into packaging materials to improve food quality and safety. Encapsulation of active compounds in bionanocomposites is done using various methods such as spray drying, spray cooling and chilling, fluidized bed coating, coacervation, liposome entrapment, co-crystallization, nanoemulsion, air suspension, freeze-drying, interfacial polymerization, molecular inclusion and sol-gel. Nonetheless, none of these methods are universally applicable for a bioactive or food component. Alternatively, lipid-based nanostructures such as liposomes and solid lipid nanoparticles have been effectively used for the delivery of bioactive molecules showing antimicrobial and antioxidant activities. Fat-soluble vitamins can be incorporated in nanoemulsions, which in addition to polymeric nanoparticles are suitable vehicles to phytochemicals like quercetin and curcumin. Nanofibers are also promising materials to incorporate bioactive substances in food packaging.