In this work we have fabricated and studied hybrid organic-inorganic nanocomposite system formed by gold nanoparticles self-assembled in organic semiconductor thin film - copper tetrafluorophthalocyanine (CuPcF$_4$). By means of Photoelectron Spectroscopy and Transmission Electron Microscopy (TEM) the evolution of the morphology and electronic structure of the system as a function of nominal gold content have been investigated. The gold atoms, deposited onto the CuPcF$_4$ surface, diffuse into the organic matrix and self-assemble to nanoparticles in a well-defined manner with a narrow size distribution, which depends on the amount of deposited gold. Using High-Resolution TEM, we were able to observe the atomic planes of single gold nanoparticles and their coalescence processes. Photoelectron spectroscopy has not revealed any detectable chemical reaction between gold and organic. However, the strong upward band bending, induced by gold nanoparticles in the organic film, takes place.