Selective modification of natural proteins is a daunting methodological challenge and a stringent test of selectivity and reaction scope. There is a continued need for new reactivity and new selectivity concepts. Transition metals exhibit a wealth of unique reactivity that is orthogonal to biological reactions and processes. As such, metal‐based methods play an increasingly important role in bioconjugation. This Review examines metal‐based methods as well as their reactivity and selectivity for the functionalization of natural proteins and peptides.