Silicon-rich silicon oxide films deposited by plasma enhanced chemical vapor deposition with different total Si contents (from 39to46at.%) have been annealed at increasing temperature (up to 1250°C) in order to study the Si nanocrystal (Si-nc) nucleation as well as the structural changes induced in the amorphous embedding matrix. The comparison between x-ray absorption measurements in total electron yield mode, Raman spectroscopy, and photoluminescence spectra allowed us to gain insight about the Si nanocrystal formation, while the chemical composition and the nature of chemical bonds into the oxidized matrix was studied by Fourier transform infrared spectroscopy. A comprehensive picture of the nucleation process has been obtained, demonstrating the active role played by the hydrogen and nitrogen atoms in the formation of Si-nc and in the thermally induced evolution of the deposited films.