In electronic devices based on hybrid materials such as nonvolatile memory elements (NVMEs), it is essential to control precisely the dispersion of metallic nanoparticles (NPs) in an insulating polymer matrix such as polystyrene in order to control the functionality of the device. In this work the incorporation of AuNPs in polystyrene films is controlled by tuning the surface functionalization of the metallic nanoparticles via ligand exchange. Two ligands with different structures were used for functionalization: 1-decanethiol and thiol-terminated polystyrene. This paper presents a versatile method for the modification of gold nanoparticles (AuNPs) with thiol-terminated polystyrene ligands via phase transfer process. An organic colloid of AuNPs (5±1 nm diameter) is obtained by the phase transfer process (from water to toluene) that allows exchanging the ligand adsorbed on AuNPs surface (hydrophilic citrate/tannic acid to hydrophobic thiols). The stability, size distribution, and precise location of modified AuNPs in the polymer matrix are obtained from UV-Vis spectroscopy, dynamic light scattering (DLS), and electron tomography. TEM tomographic 3D imaging demonstrates that the modification of AuNPs with thiol-terminated polystyrene results in homogeneous particle distribution in the polystyrene matrix compared to 1-decanethiol modified AuNPs for which a vertical phase separation with a homogeneous layer of AuNPs located at the bottom of the polymer matrix was observed.