Understanding the processes involved in the nucleation and growth of nanoparticles is essential for the development of tailored nanomaterials. Here, we investigate the solvent effects on the atomic structure and size of nanocrystalline MoO2 from a solvothermal synthesis and deduce their reaction pathways. Detailed pair distribution function (PDF) analysis reveals the formation of distinct MoO2 structures, depending on the alcohol used. We show that the atomic structure and crystallite size of the formed materials can be directly related to their formation pathway. In situ PDF together with X-ray absorption spectroscopy of the reaction between MoCl5 and an alcohol solvent allows us to see that larger nanoparticles (ca. 30 nm) with the conventional MoO2 distorted rutile structure form when the initial Cl/O-ligand exchange is fast, but the subsequent condensation and crystallization is slowed down in the synthesis process. On the other hand, when the Cl/O exchange is slowed down, a [MoIVClxOy]-complex is formed, and we obtain very small nanoparticles (2-3 nm) with the MoO2 high-pressure polymorph structure. The study shows how the chemistry of the reaction solvent affects the mechanistic pathways, and consequently the intermediate formed just prior to crystallization, which is directly applicable in the process of obtaining specific nanocrystalline materials.