Advances in nanoscience have stimulated the wide exploration of nanozymes as alternatives to enzymes. Nonetheless, nanozymes often catalyze multiple reactions and are not specialized to a specific substrate, restricting their broad application. Here, we report that the substrate selectivity of the peroxidase-mimic M–N–C can be significantly altered via forming bound intermediates with variable interactions with substrates according to the type of metal. Taking two essential reactions in chemical sensing as an example, Fe–N–C and Co–N–C showed opposite catalytic selectivity for the oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB) and 3-aminophthalhydrazide (luminol), respectively, by factors of up to 200-fold. It was revealed that specific transition metal-N coordination was the origin of the selective activation of H₂O₂ forming critically bound oxygen intermediates (MO) for oxygen-atom transfer and the consequent oxidization of substrates. Notably, owing to the embedded ligands in the rigid graphitic framework, surprisingly, the selectivity of M–N–C was even superior to that of commonly used horseradish peroxidase (HRP).