Understanding the microstructure in heterostructured nanoparticles is crucial to harnessing their properties. Although microscopy is ideal for this purpose, it allows for the analysis of only a few nanoparticles. Thus, there is a need for structural methods that take the whole sample into account. Here, a novel bulk‐approach based on the combined analysis of synchrotron X‐ray powder diffraction with whole powder pattern modeling, Rietveld and pair distribution function is presented. The microstructural temporal evolution of FeO/Fe3O4 core/shell nanocubes is studied at different time intervals. The results indicate that a two‐phase approach (FeO and Fe3O4) is not sufficient to successfully fit the data and two additional interface phases (FeO and Fe3O4) are needed to obtain satisfactory fits, i.e., an onion‐type structure. The analysis shows that the Fe3O4phases grow to some extent (≈1 nm) at the expense of the FeO core. Moreover, the FeO core progressively changes its stoichiometry to accommodate more oxygen. The temporal evolution of the parameters indicates that the structure of the FeO/Fe3O4nanocubes is rather stable, although the exact interface structure slightly evolves with time. This approach paves the way for average studies of interfaces in different kinds of heterostructured nanoparticles, particularly in cases where spectroscopic methods have some limitations.