Many proteins possess functional attributes that make them suitable for the encapsulation of bioactive agents, such as nutraceuticals and pharmaceuticals. This article reviews the state of the art of protein-based nanoencapsulation approaches. The physicochemical principles underlying the major techniques for the fabrication of nanoparticles, nanogels, and nanofibers from animal, botanical, and recombinant proteins are described. Protein modification approaches that can be used to extend their functionality in these nanocarrier systems are also described, including chemical, physical, and enzymatic treatments. The encapsulation, retention, protection, and release of bioactive agents in different protein-based nanocarriers are discussed. Finally, some of the major challenges in the design and fabrication of protein-based delivery systems are highlighted.