The electron-phonon interaction is of central importance for the electrical and thermal properties of solids, and its influence on superconductivity, colossal magnetoresistance and other many-body phenomena in correlated-electron materials is the subject of intense research at present. However, the non-local nature of the interactions between valence electrons and lattice ions, often compounded by a plethora of vibrational modes, presents formidable challenges for attempts to experimentally control and theoretically describe the physical properties of complex materials. Here we report a Raman scattering study of the lattice dynamics in superlattices of the high-temperature superconductor YBa2Cu3O7 (YBCO) and the colossal-magnetoresistance compound La2/3Ca1/3MnO3 that suggests a new approach to this problem. We find that a rotational mode of the MnO6 octahedra in La2/3Ca1/3MnO3 experiences pronounced superconductivity-induced line-shape anomalies, which scale linearly with the thickness of the YBCO layers over a remarkably long range of several tens of nanometres. The transfer of the electron-phonon coupling between superlattice layers can be understood as a consequence of long-range Coulomb forces in conjunction with an orbital reconstruction at the interface. The superlattice geometry thus provides new opportunities for controlled modification of the electron-phonon interaction in complex materials.