Magnetic spinel ferrite MFe2O4 (M = Mn, Co, Ni, Zn) nanoparticles have been prepared via simple, green and scalable hydrothermal synthesis pathways utilizing sub- and supercritical conditions to attain specific product characteristics. The crystal-, magnetic- and micro-structures of the prepared crystallites have been elucidated through meticulous characterization employing several complementary techniques. Analysis of energy dispersive X-ray spectroscopy (EDS) and X-ray absorption near edge structure (XANES) data verifies the desired stoichiometries with divalent M and trivalent Fe ions. Robust structural characterization is carried out by simultaneous Rietveld refinement of a constrained structural model to powder X-ray diffraction (PXRD) and high-resolution neutron powder diffraction (NPD) data. The structural modeling reveals different affinities of the 3d transition metal ions for the specific crystallographic sites in the nanocrystallites, characterized by the spinel inversion degree, x, [M2+ 1−xFe3+ x]tet[M2+ xFe3+ 2−x]octO4, compared to the well-established bulk structures. The MnFe2O4 and CoFe2O4 nanocrystallites exhibit random disordered spinel structures (x = 0.643(3) and 0.660(6)), while NiFe2O4 is a completely inverse spinel (x = 1.00) and ZnFe2O4 is close to a normal spinel (x = 0.166(10)). Furthermore, the size, size distribution and morphology of the nanoparticles have been assessed by peak profile analysis of the diffraction data, transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM). The differences in nanostructure, spinel inversion and distinct magnetic nature of the M2+ ions directly alter the magnetic structures of the crystallites at the atomic-scale and consequently the macroscopic magnetic properties of the materials. The present study serves as an important structural benchmark for the rapidly expanding field of spinel ferrite nanoparticle research.