Control over the quantum states of a massive oscillator is important for several technological applications and to test the fundamental limits of quantum mechanics. Addition of an internal degree of freedom to the oscillator could be a valuable resource for such control. Recently, hybrid electromechanical systems using superconducting qubits, based on electric-charge mediated coupling, have been quite successful. Here, we realize a hybrid device, consisting of a superconducting transmon qubit and a mechanical resonator coupled using the magnetic-flux. The coupling stems from the quantum-interference of the superconducting phase across the tunnel junctions. We demonstrate a vacuum electromechanical coupling rate up to 4 kHz by making the transmon qubit resonant with the readout cavity. Consequently, thermal-motion of the mechanical resonator is detected by driving the hybridized-mode with mean-occupancy well below one photon. By tuning qubit away from the cavity, electromechanical coupling can be enhanced to 40 kHz. In this limit, a small coherent drive on the mechanical resonator results in the splitting of qubit spectrum, and we observe interference signature arising from the Landau–Zener–Stückelberg effect. With improvements in qubit coherence, this system offers a novel platform to realize rich interactions and could potentially provide full control over the quantum motional states.