Nowadays, natural materials as smart building blocks for assembling functional materials have aroused extensive interest in the scientific community. Proteins and polyphenols are typical natural building blocks that are widely used. On the one hand, proteins are one of the most versatile classes of biomolecules, serving as catalysts, signaling molecules, transporters, receptors, scaffolds that maintain the integrity of cell and tissue, and more. On the other hand, the facile adhesion of naturally abundant polyphenols with other substances and their potential biomedical applications have been highly attractive for functional biomaterials fabrication. Additionally, there are a variety of interactions between the proteins and polyphenols, mainly hydrogen bonding, hydrophobic, and ionic interactions. These reversible dynamic interactions enable proteins and polyphenols to form stable protein-polyphenol assemblies and maintain their inherent structures and biological activities in the assemblies. Therefore, protein-polyphenol assemblies can be applied to design a variety of advanced functional materials for biomedical applications. Herein, recent progress in protein-polyphenol particles, capsules, coatings, and hydrogels is summarized, the preparation and application of these assemblies are introduced in detail, and the future of the field is prospected.