The atomic structure of nanoparticles can be easily determined by transmission electron microscopy. However, obtaining atomic-resolution chemical information about the individual atomic columns is a rather challenging endeavor. Here, crystalline monodispersed spinel FeO/MnO core-shell nanoparticles have been thoroughly characterized in a high-resolution scanning transmission electron microscope. Electron energy-loss spectroscopy (EELS) measurements performed with atomic resolution allow the direct mapping of the Mn/Mn ions in the shell and the Fe/Fe in the core structure. This enables a precise understanding of the core-shell interface and of the cation distribution in the crystalline lattice of the nanoparticles. Considering how the different oxidation states of transition metals are reflected in EELS, two methods of performing a local evaluation of the cation inversion in spinel lattices are introduced. Both methods allow the determination of the inversion parameter in the iron oxide core and manganese oxide shell, as well as detecting spatial variations in this parameter, with atomic resolution. X-ray absorption measurements on the whole sample confirm the presence of cation inversion. These results present a significant advance toward a better correlation of the structural and functional properties of nanostructured spinel oxides.