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The thermal-induced diffusion at nanoscale is investigated through the detailed study of the structural and magnetic properties of Co@Au nanoparticles as a function of the deposition temperature. Nanoparticles of 10 nm were fabricated using an ion cluster source from a Co95Au5 target. While low-temperature deposition leads to the formation of an alloyed fcc CoAu core with an incomplete cobalt oxide shell, higher deposition temperature induces the formation of a pure hcp Co core with an intermediate Au shell and a compact outer cobalt oxide shell. The evolution of the magnetic properties of the nanoparticles is presented and discussed in light of the structural changes of the nanoparticles upon deposition temperature and nanoparticle density. It is found that thermal-induced diffusion can be successfully used to tune the structural and magnetic properties at the nanoscale in Co Au nanoparticles.