Iron oxide nanoparticles with a wüstite structure have been prepared by thermal decomposition. In air, they undergo a spontaneous transition into a thermodynamically more stable magnetite structure that grows from the surface. The thickness of this magnetite shell increases with time, thereby producing a series of core-shell nanoparticles. We investigated the kinetics of this phase transition in 23 nm nanocubes using time-resolved XRD, from which the fractions of individual phases were determined by the Rietveld refinement. This kinetics is described theoretically using three coupled reaction-diffusion master equations for the concentrations of oxygen, wüstite, and magnetite, in which both the diffusion of oxygen and its reaction with wüstite are thermally activated. The coefficients of these terms were adjusted so that the predictions of the model reproduce the XRD data at 298 K and 353 K, whereas the predictive capability of the model was assessed by comparing its predictions with measurements at 403 K.