A novel step-wise approach for fabrication of periodic arrays of two different types of nanoparticles (NPs), selectively localized at different block copolymer phases is demonstrated. In the first step, pre-synthesized ≈12 nm silver nanoparticles (AgNPs), stabilized with thiol-terminated polystyrene, are mixed with poly(styrene-block-vinylpyridine) (PS-b-PVP) block copolymer in a common solvent. After film casting and consequent solvent vapor annealing the AgNPs are selectively localized within the PS phase of the block copolymer matrix due to the interaction with PS shell of the nanoparticles. In the second step, ≈2–5 nm gold, platinum, or palladium nanoparticles are directly deposited from their aqueous dispersion on the PVP domains of the self-assembled block copolymer thin films. In such a way, thin films of nanostructured block copolymer with two types of nanoparticles, separated by the two distinct block copolymer phases, are prepared in a step-wise manner. The presented method is very simple and can be applied for various combinations of pre-synthesized nanoparticles where the characteristics of either type of nanoparticles are tuned accordingly in advance, which is more difficult to achieve for in situ synthesized nanoparticles.