Neutron and X-ray powder diffraction have been used to investigate the differences between the crystal growth of ferrite magnetic nanoparticles (MFe₂O₄withM= Mn, Fe, Co, Ni, Zn) by two methodologies: microwave radiation and thermal decomposition routes. Rietveld refinement has been used to extract the cationic distribution, the microstructure and magnetic information. Results for the nanoparticles produced by the two procedures evidence similar cationic distribution, microstructure and magnetic properties: complete cationic disorder forM= Mn and Co, crystal size around/below 10 nmetc. It is thus proven that microwave-assisted growth is a promising eco-friendly synthetic technique for the generation of high-quality nanocrystals with comparable structure and properties to those produced by the thermal methodology, even though the microwave route needs a shorter time and lower annealing temperature to obtain the final crystal nanoparticles.