The magnetic properties of spinel ferrites (MFe2O4, M = Mn, Fe, Co, Ni, Zn, etc.) are largely determined by the type of divalent cation, M2+ and cation distribution between the tetrahedral and octahedral sites in the structure. Partial substitution of Zn2+ into the thermodynamically preferred tetrahedral coordination in ferrites produces an increase in magnetic saturation at room temperature. However, nanosized crystallites are known to adopt different structures compared to their bulk equivalents. Consequently, reliable characterization of the atomic structure of nanosized ferrites is essential for understanding and tailoring their magnetic properties. Here, we present a meticulous study of the crystal-, magnetic- and micro-structures of mixed ZnxCo1−xFe2O4 spinel ferrite nanocrystallites in the entire composition range (x = 0.0–1.0 in steps of 0.1). Gram-scale nanoparticle preparation was performed via the widely used hydrothermal method. Eight compositions were selected to study the effect of 4 hours vacuum annealing at 823 K. Combined Rietveld refinement of powder X-ray and neutron diffraction data along with Mössbauer analysis reveal how the as-synthesized nanocrystallites adopt metastable cation inversions, different from the well-established and thermodynamically stable inversions of the bulk equivalents. The annealing treatment causes the structure of the crystallites to relax towards a more bulk-like cation distribution. For all compositions, the smaller as-synthesized nanocrystallites with metastable cation inversion exhibit a higher saturation magnetization compared to the annealed samples. The demonstrated control over the spinel ferrite cation distribution is a key step on the way to designing cheap magnetic materials with tunable properties optimized for specific applications.