The atomic level structure of a series of monodisperse single crystalline nanoparticles with a magnetic core of manganese ferrite was studied using X-ray absorption fine structure (EXAFS) and X-ray absorption near edge structure (XANES) techniques at both the Fe and Mn K-edges, and conventional and high resolution transmission electron microscopy (TEM and HRTEM). In particular, insights on the non-stoichiometry and on the inversion degree of manganese ferrite nanocrystals of different size were obtained by the use of complementary structural and spectroscopic characterization techniques. The inversion degree of the ferrite nanocrystals, i.e. the cation distribution between the octahedral and tetrahedral sites in the spinel structure, was found to be much higher (around 0.6) than the literature values reported for bulk stoichiometric manganese ferrite (around 0.2). The high inversion degree of the nanoparticles is ascribed to the partial oxidation of Mn(2+) to Mn(3+) which was evidenced by XANES, leading to non-stoichiometric manganese ferrite.