The late‐stage functionalization of peptides and proteins holds significant promise for drug discovery and facilitates bioorthogonal chemistry. This selective functionalization leads to innovative advances in in vitro and in vivo biological research. However, it is a challenging endeavor to selectively target a certain amino acid or position in the presence of other residues containing reactive groups. Biocatalysis has emerged as a powerful tool for selective, efficient, and economical modifications of molecules. Enzymes that have the ability to modify multiple complex substrates or selectively install nonnative handles have wide applications. Herein, we highlight enzymes with broad substrate tolerance that have been demonstrated to modify a specific amino acid residue in simple or complex peptides and/or proteins at late‐stage. The different substrates accepted by these enzymes are mentioned together with the reported downstream bioorthogonal reactions that have benefited from the enzymatic selective modifications. Biocatalysis is a powerful tool to achieve selective modifications on peptides with strong potential in the development of pharmaceuticals and in biological research. This review focuses on amino acid residue‐specific enzymes with broad substrate tolerance as well as their nonnative substrates. These enzymes have enabled the modification of a wide range of peptides and proteins at late‐stage.