The electronic, morphological and structural properties of WO3 thin films, synthesized via a sol–gel route and deposited on ITO/glass substrates by spin-coating, were analyzed as a function of annealing temperature (100–700 °C range) by Scanning Electron Microscopy, Atomic Force Microscopy, micro-Raman spectroscopy, X-ray Diffraction and Photoelectron Spectroscopy. We have found evidence of two competing processes when the film is annealed at high temperatures (600–700 °C): a structural phase transition from amorphous to crystalline WO3 and a temperature-activated diffusion of sodium ions, from the substrate into the WO3 film, which induces the formation of sodium tungstate. The surface of the films was found to be oxygen deficient after deposition but reverted to fully oxidized WO3 after high temperature annealing in air. The annealing also induced a restructuring of the films with formation of nano-crystalline aggregates. The influence of film thickness on these processes was also investigated.