The crystallization pathway of indium tin oxide nanoparticles during solvothermal synthesis in benzyl alcohol was investigated. The synthesis was stopped after different reaction times in the range of 1–24 h, and the structural and morphological characteristics of the products were analyzed by powder X-ray diffraction, electron microscopy, and UV/Vis spectroscopy. Interestingly, the crystallization mechanism does not proceed along a simple nucleation and growth pathway, but involves a two-step process. In the first 12 h an intermediate phase is formed, which consists of nanocrystallites 3–6 nm in size stabilized by an organic matrix. In this organic–inorganic network the nanoparticles are aligned into superstructures, but without any crystallographic orientation. After 12 h the intermediate phase is abruptly transformed into indium tin oxide nanoparticles with the bixbyite structure and with crystallite sizes of about 10–12 nm. This step is accompanied by the disappearance of the organic phase and the loss of the superstructure.