Nanotechnology offers immense opportunities for regulating and improving biological functions of proteins in vitro. Recent years have witnessed growing efforts to develop protein-incorporated hybrid nanostructured materials with potential applications in functional materials, enzymatic catalysis, drug delivery, and analytical sciences. In this review, recent advances in functional protein-organic/inorganic hybrid nanomaterials are discussed with an emphasis on the novel preparation methods, resulting nanostructures, and their potential applications in drug delivery and enzymatic catalysis. Future directions toward the rational design of these bionanomaterials are suggested.