Development of a new strategy for site-specific protein modification can expand the range of applications of functional proteins in biotechnology. In particular, the site-specific attachment of proteins onto a solid surface is a prerequisite for the contruction of functional biomaterials involving an interface such as biosensors and biochips. To avoid protein denaturation upon the formulation processes, we have focused on the use of an enzyme that recognizes proteins as substrates. The key enzyme we focused in this study is microbial transglutaminase (MTG) that catalyzes covalent bond formation between the side chains of glutamine and lysine residues that fit to the substrate specificity of this enzyme. First, enzymatic protein immobilization was validated using several recombinant proteins tagged with N- or C-terminal specific peptide tag for MTG as a model. Secondary, a proteinaceous nanoparticle prepared with MTG was characterized as a biodegradable nanocarrier for hydrophobic substances. The present study shows a potential of enzymatic approach to create a variety of protein-based biomaterials for application in nano-biotechnology.