The intimate relationship between stoichiometry and physicochemical properties in transition-metal oxides makes them appealing as tunable materials. These features become exacerbated when dealing with nanostructures. However, due to the complexity of nanoscale materials, establishing a distinct relationship between structure-morphology and functionalities is often complicated. In this regard, in the FexO/Fe3O4 system a largely unexplained broad dispersion of magnetic properties has been observed. Here we show, thanks to a comprehensive multi-technique approach, a clear correlation between the magneto-structural properties in large (45 nm) and small (9 nm) FexO/Fe3O4 core/shell nanoparticles that can explain the spread of magnetic behaviors. The results reveal that while the FexO core in the large nanoparticles is antiferromagnetic and has bulk-like stoichiometry and unit-cell parameters, the FexO core in the small particles is highly non-stoichiometric and strained, displaying no significant antiferromagnetism. These results highlight the importance of ample characterization to fully understand the properties of nanostructured metal oxides.