Germanium dioxide (GeO2) is a versatile material with several different crystalline polymorphs and interesting applications in, e.g., optics, microelectronics, and Li-ion batteries. In particular, many of the material’s properties depend on the size of the prepared crystallites, and thus, nanocrystalline GeO2 is of special interest. Here, GeO2 nanoparticles are prepared via sol–gel processes by the hydrolysis of Ge isopropoxide (Ge(OCH(CH3)2)4). The precipitated powders are dried at room temperature and annealed in ambient air using temperatures between 500 °C and 1000 °C from 3 to 24 h. The samples were characterized by X-ray diffraction, X-ray absorption fine structure spectroscopy, and scanning electron microscopy, providing the crystalline structures, the phase composition, as well as the morphology and crystallite size of the formed particles and their changes upon heating. According to the structural analysis, the samples are crystalline with a dominant β- (low temperature) quartz phase without any heat treatment directly after drying and increasing contributions of α- (high-temperature modification) quartz and quartz-like GeO2 structures with increasing temperature and annealing time were found. According to electron microscopy and the X-ray analysis, the particle size ranges from about 40 to 50 nm for the pristine particles and to about 100 nm and more for the annealed materials.