AbstractA single spin in a Josephson junction can reverse the flow of the supercurrent by changing the sign of the superconducting phase difference across it. At mesoscopic length scales, these π-junctions are employed in various applications, such as finding the pairing symmetry of the underlying superconductor, as well as quantum computing. At the atomic scale, the counterpart of a single spin in a superconducting tunnel junction is known as a Yu–Shiba–Rusinov state. Observation of the supercurrent reversal in that setting has so far remained elusive. Here we demonstrate such a 0 to π transition of a Josephson junction through a Yu–Shiba–Rusinov state as we continuously change the impurity–superconductor coupling. We detect the sign change in the critical current by exploiting a second transport channel as reference in analogy to a superconducting quantum interference device, which provides our scanning tunnelling microscope with the required phase sensitivity. The measured change in the Josephson current is a signature of the quantum phase transition and allows its characterization with high resolution.