The first stages of the nucleation and growth of silica nanoparticles are followed in situ using both SAXS and Raman spectroscopy. Coupling these two techniques allows the determination of the fractions of soluble and solid silica as a function of the reaction time. SAXS also enables demonstrating that major modifications of the structure occur after the initial precipitation period, inducing an increase of the precipitate density. These structural modifications have important implications in the initial nucleation growth stages, which have never been introduced either in classical models or in more recent kinetic nucleation theories. Such restructuration stages could contribute to explain the monodispersity of the obtained silica nanoparticles that is not predicted by classical models.