The control of the phase distribution in multicomponent nanomaterials is critical to optimize their catalytic performance. In this direction, while impressive advances have been achieved in the past decade in the synthesis of multicomponent nanoparticles and nanocomposites, element rearrangement during catalyst activation has been frequently overseen. Here, we present a facile galvanic replacement-based procedure to synthesize Co@Cu nanoparticles with narrow size and composition distributions. We further characterize their phase arrangement before and after catalytic activation. When oxidized at 350 °C in air to remove organics, Co@Cu core-shell nanostructures oxidize to polycrystalline CuO-Co3O4 nanoparticles with randomly distributed CuO and Co3O4 crystallites. During a posterior reduction treatment in H2 atmosphere, Cu precipitates in a metallic core and Co migrates to the nanoparticle surface to form Cu@Co core-shell nanostructures. The catalytic behavior of such Cu@Co nanoparticles supported on mesoporous silica was further analyzed toward CO2 hydrogenation in real working conditions.