X-ray reflectometry, X-ray diffraction and grazing incidence small angle X-ray scattering have been complementary used to fully characterize zirconia (ZrO2) thin films obtained by the sol–gel route. The films were synthesized on various sapphire (Al2O3), silicon (Si) and glass mirror-polished wafers by a dip-coating process in a zirconia precursor sol. Versus the synthesis parameters as alkoxide sol concentration, withdrawal speed and annealing temperature, the microstructure of the layer is managed and its different microstructural parameters such as thickness, mass density, crystalline phase, grain size and spatial arrangement have been determined. The as prepared layers are amorphous. During a thermal treatment at low temperature (< 1000 °C), the layers thickness decreases while their mass density increases. Simultaneously the zirconia precursor crystallises in the zirconia tetragonal form and the coating is made of randomly oriented nanocrystals which self organise in a dense close-packed microstructure. At low temperature, this microstructural evolution is similar whatever the substrate. Moreover, the layer evolves as the corresponding bulk xerogel showing that the presence of the interface does not modify the thermal microstructure evolution of the layer which is controlled by a normal grain growth leading to relatively dense nanocrystalline thin films.