Nanocomposites consisting of noble metal nanoparticles (NPs) embedded in TiO2 thin films are of great interest for applications in optoelectronics, photocatalysis and solar-cells for which the plasmonic properties of the metal NPs play a major role. This work investigates the first stages of the formation of gold NPs by thermal annealing of Au-doped TiO2 thin films grown by magnetron sputtering. A low concentration of gold in the films is considered (5 at.%) in order to study the first stages of the formation of the NPs. Raman spectroscopy is used to follow the crystallization of TiO2 when increasing the annealing temperature. In addition, low-frequency Raman scattering (LFRS) is used to investigate the formation of gold NPs and to determine their size. Resonant LFRS measurements obtained by using a laser wavelength matching the surface plasmon resonance of the metallic NPs significantly enhances the Raman peak intensity enabling to focus on the first stages of the NPs formation. A double size distribution is observed at Ta = 800 °C calling for additional investigations by transmission electron microscopy (TEM). TEM observations reveal an inhomogeneous in-depth size distribution of gold NPs. The annealed films are structured in two sublayers with bigger NPs at the bottom and smaller NPs at the top. At Ta = 800 °C, a double size distribution is confirmed near the surface. A mechanism is proposed to explain the formation of the sublayers. The modification of the diffusion of gold atoms by stresses in the film near the substrate is assumed to be responsible for the observed two layers structure.