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-Stuckelberg 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.