Structural changes of Ni-Au core-shell nanoparticles with increasing temperature are studied at atomic resolution. The bimetallic clusters, synthesized in superfluid helium droplets, show a centralized Ni core, which is an intrinsic feature of the growth process inside helium. After deposition on SiN x , the nanoparticles undergo a programmed temperature treatment in vacuum combined with an in situ transmission electron microscopy study of structural changes. We observe not only full alloying far below the actual melting temperature, but also a significantly higher stability of core-shell structures with decentralized Ni cores. Explanations are provided by large-scale molecular dynamics simulations on model structures consisting of up to 3000 metal atoms. Two entirely different diffusion processes can be identified for both types of core-shell structures, strikingly illustrating how localized, atomic features can still dictate the overall behavior of a nanometer-sized particle.