Amorphous Nb2O5 thin films of three different thicknesses (10, 100, 400 nm) were deposited onto SiO2/Si substrates by reactive sputtering in an Ar–O2 plasma. Thermal treatments were performed at different temperatures between 500 and 1100 °C. The structural and morphological evolution with temperature is shown to be dependent on the film thickness. At 600 °C, the films essentially crystallize in the TT phase. On the thickest films, the T phase also appears. Annealing at higher temperature progressively increases the concentration of the T phase. The films show large flat grains extending over the whole film thickness. In addition, a large number of polyhedral bubbles is present in the 100 and 400 nm films due to Ar atoms trapped during sputtering. After annealing at 1100 °C the Ar bubbles are no longer present and partial diffusion of the films into the substrate is observed. The modification at high temperature, explained either by the M or the H phase, is favored on the thickest films and leads to plate shaped grains.