Magnetite (Fe3O4) is of fundamental importance for the Verwey transition near TV = 125 K, below which a complex lattice distortion and electron orders occur. The Verwey transition is suppressed by chemical doping effects giving rise to well-documented first and second-order regimes, but the origin of the order change is unclear. Here, we show that slow oxidation of monodisperse Fe3O4 nanoparticles leads to an intriguing variation of the Verwey transition: an initial drop of TV to a minimum at 70 K after 75 days and a followed recovery to 95 K after 160 days. A physical model based on both doping and doping-gradient effects accounts quantitatively for this evolution between inhomogeneous to homogeneous doping regimes. This work demonstrates that slow oxidation of nanoparticles can give exquisite control and separation of homogeneous and inhomogeneous doping effects on the Verwey transition and offers opportunities for similar insights into complex electronic and magnetic phase transitions in other materials.