Graphene, as well as other two-dimensional materials, is a promising candidate for use in bioimaging, therapeutic drug delivery, and bio-sensing applications. Here, we developed a protocol to functionalize graphene with recombinant proteins using genetically encoded SpyTag-SpyCatcher chemistry. SpyTag forms a covalent isopeptide bond with its genetically encoded partner SpyCatcher through spontaneous amidation under physiological conditions. The functionalization protocol developed is based on the use of short proteins as a linker, where two graphene-binding-peptides (GBPs) are attached to both ends of SpyTag (referred to as GStG), followed by the covalent conjugation with SpyCatcher-fusion proteins. The proposed method enables the decoration of crystalline graphene with various proteins, such as fluorescent proteins and affibody molecules that bind to cancerous cells. This scheme, which takes advantage of the cleanness of single-crystal graphene and the robustness of SpyTag-SpyCatcher chemistry, provides a versatile platform on which to study the biomolecule-surface and cell-substrate interactions and, indeed, may lead to a new way of designing biomedical devices. The interaction between peptides and graphene was clearly shown using molecular dynamics simulation and proven using specially designed experiments.