The thermal decomposition of organometallic precursors in the presence of surfactants and a long-chain alcohol is a valuable method to synthesize magnetic nanoparticles (MNPs) because it provides good control of the final morphology and crystallinity of the magnetic material. These parameters, and consequently the magnetic properties, depend on several details of the experimental procedure of chemical synthesis. We have studied the role of the pre-decomposition step, heating the system to 373–393 K in inert gas flux, on the final composition and morphology of the system. By adding this intermediate step, we were able to produce MNPs with a Fe1-yO/Fe3O4 core–shell structure and sizes of 20–25 nm. When the same synthesis protocol was used skipping the pre-decomposition stage, monophasic MNPs of 11 nm with ferrite structure were obtained. These differences in the composition have a major effect on the resulting magnetic properties of MNPs, and are related to some by-reactions in the synthesis solution during the preparation procedure.