The atomic structure and interfaces of CdS/Cu2S heterostructured nanorods are investigated with the aberration-corrected TEAM 0.5 electron microscope operated at 80 kV and 300 kV applying in-line holography and complementary techniques. Cu2S exhibits a low-chalcocite structure in pristine CdS/Cu2S nanorods. Under electron beam irradiation the Cu2S phase transforms into a high-chalcocite phase while the CdS phase maintains its wurtzite structure. Time-resolved experiments reveal that Cu+–Cd2+ cation exchange at the CdS/Cu2S interfaces is stimulated by the electron beam and proceeds within an undisturbed and coherent sulfur sub-lattice. A variation of the electron beam current provides an efficient way to control and exploit such irreversible solid-state chemical processes that provide unique information about system dynamics at the atomic scale. Specifically, we show that the electron beam-induced copper–cadmium exchange is site specific and anisotropic. A resulting displacement of the CdS/Cu2S interfaces caused by beam-induced cation interdiffusion equals within a factor of 3–10 previously reported Cu diffusion length measurements in heterostructured CdS/Cu2S thin film solar cells with an activation energy of 0.96 eV.