Protein hydrogels constructed from recombinant proteins have attracted increasing interests for fundamental biological studies as well as applications in biomedical engineering field. In such protein hydrogels, biochemical and physical properties of protein hydrogels are often coupled to each other, making it challenging to investigate the individual effect of chemical and physical cues on cells. Moreover, laborious engineering is often required to incorporate different protein ligands into such hydrogels. To address these challenges, functionalizing a blank slate protein hydrogel is an attractive approach. However, conjugating ligands to such a blank slate protein hydrogel is challenging, as existing bioconjugation methods developed in synthetic polymer hydrogels cannot be readily adapted for protein hydrogels, significantly impeding the use of this approach in the field. Here we report a facile, general, and robust method, which is based on the SpyCatcher-SpyTag chemistry, to covalently functionalize the "blank slate" of protein hydrogels using genetically encoded interacting partners. We demonstrate that this novel method enables covalent conjugation of a wide variety of ligands, including full-length intact folded proteins, to a blank slate protein hydrogel, and allows for the decoupling of biochemical and physical properties of hydrogels from each other and investigating the individual effect of biochemical and mechanical cues on cell behaviors. To our best knowledge, this is the first general approach enabling functionalization of protein hydrogels, and we anticipate that this novel approach will find a broad range of uses in protein-based biomaterials for applications in biomedical engineering.