The observation of the quantum states of motion of a macroscopic mechanical structure remains an open challenge in quantum-state preparation and measurement. One approach that has received extensive theoretical attention^,,,,,,,,,,,, is the integration of superconducting qubits as control and detection elements in nanoelectromechanical systems (NEMS). Here we report measurements of a NEMS resonator coupled to a superconducting qubit, a Cooper-pair box. We demonstrate that the coupling results in a dispersive shift of the nanomechanical frequency that is the mechanical analogue of the ‘single-atom index effect’ experienced by electromagnetic resonators in cavity quantum electrodynamics. The large magnitude of the dispersive interaction allows us to perform NEMS-based spectroscopy of the superconducting qubit, and enables observation of Landau–Zener interference effects—a demonstration of nanomechanical read-out of quantum interference.