A promising approach of making high quality contacts on semiconductors is a silicidation (for silicon) or germanidation (for germanium) annealing process, where the metal enters the semiconductor and creates a low resistance intermetallic phase. In a nanowire, this process allows one to fabricate axial heterostructures with dimensions depending only on the control and understanding of the thermally induced solid-state reaction. In this work, we present the first observation of both germanium and copper diffusion in opposite directions during the solid-state reaction of Cu contacts on Ge nanowires using in situ Joule heating in a transmission electron microscope. The in situ observations allow us to follow the reaction in real time with nanometer spatial resolution. We follow the advancement of the reaction interface over time, which gives precious information on the kinetics of this reaction. We combine the kinetic study with ex situ characterization using model-based energy dispersive X-ray spectroscopy (EDX) indicating that both Ge and Cu diffuse at the surface of the created Cu3Ge segment and the reaction rate is limited by Ge surface diffusion at temperatures between 360 and 600 °C. During the reaction, germanide crystals typically protrude from the reacted NW part. However, their formation can be avoided using a shell around the initial Ge NW. Ha direct Joule heating experiments show slower reaction speeds indicating that the reaction can be initiated at lower temperatures. Moreover, they allow combining electrical measurements and heating in a single contacting scheme, rendering the Cu–Ge NW system promising for applications where very abrupt contacts and a perfectly controlled size of the semiconducting region is required. Clearly, in situ TEM is a powerful technique to better understand the reaction kinetics and mechanism of metal–semiconductor phase formation.