As the advantageous properties of nanoparticles (NPs) often emerge only when appropriate coupling and exchange phenomena between the NPs can take place, the control of the inter-particle distance, regular ordering, and location of the nanoparticles onto solid supports is a critical issue. A robust method to control the spatial organization of NPs onto solid supports, based on the use of self-assembling di-block copolymers (BCPs) as structure-guiding material, is reported. Two different polystyrene-b-poly(methyl methacrylate) (PS-b-PMMA) BCPs, characterized by a different PS volume fraction, were used as matrices for the fabrication of nanocomposite thin films with cylindrical and lamellar morphologies controlled at the nanoscale. Selective inclusion of surface functionalized gold (Au) and zinc oxide (ZnO) NPs of appropriate size in the PS nanodomains was achieved from dispersions of the BCPs and NPs in a common solvent. The orientation of the BCPs cylinder and lamellar nanodomains in spin-coated thin films was controlled by solvent and thermal annealing protocols, coupled with techniques of surface neutralization.