Fabricating subnanometre-thick core-shell nanocatalysts is effective for obtaining high surface area of an active metal with tunable properties. The key to fully realize the potential of this approach is a reliable synthesis method to produce atomically ordered core-shell nanoparticles. Here we report new insights on eliminating lattice defects in core-shell syntheses and opportunities opened for achieving superior catalytic performance. Ordered structural transition from ruthenium hcp to platinum fcc stacking sequence at the core-shell interface is achieved via a green synthesis method, and is verified by X-ray diffraction and electron microscopic techniques coupled with density functional theory calculations. The single crystalline Ru cores with well-defined Pt bilayer shells resolve the dilemma in using a dissolution-prone metal, such as ruthenium, for alleviating the deactivating effect of carbon monoxide, opening the door for commercialization of low-temperature fuel cells that can use inexpensive reformates (H2 with CO impurity) as the fuel.