As the pioneering Fe3O4 nanozymes, their explicit peroxidase (POD)-like catalytic mechanism remains elusive. Although many studies have proposed the surface Fe2+-induced Fenton-like reactions accounting for their POD-like activity, few focus on the internal atomic changes and their contribution to the catalytic reaction. Here we report that Fe2+ within Fe3O4 transfers electrons to the surface via the Fe2+-O-Fe3+ chain, regenerating the surface Fe2+ and enabling a sustained POD-like catalytic reaction. This process occurs with the outward migration of excess oxidized Fe3+ from the lattice, which is a rate-limiting step. After prolonged catalysis, Fe3O4 nanozymes suffer the phase transformation to γ-Fe2O3 with a depletable POD-like activity. This self-depleting characteristic of nanozymes with internal atoms involved in electrons transfer and ion migration is well-validated on lithium iron phosphate nanoparticles. We reveal a key yet ever ignored issue concerning the necessity of considering both surface and internal atoms when designing, modulating, and applying nanozymes.