The structure of Mn0.5Zn0.5Fe2O4 spinel ferrite nanoparticles is studied as a function of their size and the experimental conditions of their synthesis using X-ray absorption spectroscopy. The nanoparticles of different sizes down to approximately 2 nm and with a narrow size distribution were synthesized using co-precipitation in reverse microemulsions. Simultaneous refinement of the X-ray absorption fine structure (EXAFS) of three constituting metals shows a migration of Mn and Zn ions to the octahedral site of the spinel lattice compensated by the corresponding migration of the Fe ions. To a smaller extent, Mn ions switch the occupation site already in bulk and in larger nanoparticles, while a sporadic migration of Zn is detected only in the nanoparticles with sizes below approximately 5 nm. X-ray absorption near edge structure (XANES) reveals considerable variations in the position of the Mn K edge, suggesting the average Mn valence in the nanoparticles to be higher than 3+. Annealing at 500 °C relaxes the structure of as-synthesized nanoparticles toward the structure of the ceramic bulk standard.