We have investigated the paramagnetic defects and the structure of magnetron sputtered amorphous SiO2 films containing 3.8 at. % Ge (a-SiO2:Ge) over the 500–1000 °C annealing temperature range using electron paramagnetic resonance (EPR), Fourier-transform infrared (FTIR) absorption, and transmission electron microscopy (TEM). The EPR spectra of as-grown a-SiO2:Ge films reveal three different defects: Si-E′ centers with g||=2.0019 and g⊥=2.0004, •Ge≡Si3 dangling bonds with g||=2.001 and g⊥=2.024, and •Si≡Si2O or •Si≡SiO2 defects with g=2.004. While the Si-E′ and g=2.004 lines are removed by heat treatments at 500 °C, the signal from •Ge≡Si3 dangling bonds persists up to annealing temperatures of 700 °C. The structural changes induced upon annealing on the a-SiO2:Ge films have been studied by monitoring the frequency and linewidth of the asymmetric stretching vibration of th- e Si–O–Si linkage using FTIR. We find that the rearrangement of the amorphous oxide network occurs primarily within the 500–700 °C temperature range and no further significant recovery happens upon annealing at temperatures above 700 °C, in line with the EPR results. TEM images reveal the formation of Ge nanocrystals (Ge ncs) with diameters of 2–4 nm already upon heat treatments at 500 °C. Moreover, it is shown that the mean size of the Ge ncs increases quite significantly as the temperature of the heat treatments increases. The mean diameter of Ge ncs observed after annealing at temperatures above 600 °C is above that expected for Ge ncs with efficient photoluminescence properties. The implications of our experimental results for the understanding of the quenching of the photoluminescence from quantum-confined excitons within Ge ncs are briefly discussed.