Molecular dynamics simulations have been employed to investigate the thermodynamic behavior of Co domains with characteristic size of about 3 nm embedded in a crystalline Cu matrix. Co domains are seen to undergo a hcp-to-fcc transition at temperatures dependent on the relative orientation between the Co and Cu crystalline lattices, as well as on the pressure and stress conditions applied to the matrix. No orientation effect is observed at null external pressure and stress. The transition temperature increases instead with the pressure according to a univocal trend, whereas the effect of uniaxial stress depends on the relative orientation of the Co and Cu lattices.