physics. Yet, quantum control of such systems remains challenging, particularly owing to their low energy scale and the difficulty of achieving efficient coupling to other well-controlled quantum devices. Here, we demonstrate repeated, and high-fidelity interactions between a 4 MHz suspended silicon nitride membrane and a resonant superconducting heavy-fluxonium qubit. The qubit is initialized at an effective temperature of 27~μK and read out in a single-shot with 77% fidelity. During the membrane’s 6~ms lifetime, the two systems swap excitations more than 300 times. After each interaction, a state-selective detection is performed, implementing a stroboscopic series of weak measurements that provide information about the mechanical state. The accumulated records reconstruct the membrane’s position noise-spectrum, revealing both its thermal occupation nth≈47 at 10~mK and the qubit-induced back-action. By preparing the qubit either in its ground or excited state before each interaction, we observe an imbalance between the emission and absorption spectra, proportional to nth and nth+1, respectively-a hallmark of the non-commutation of phonon creation and annihilation operators. Since the predicted Diósi-Penrose gravitational collapse time is comparable to the measured mechanical decoherence time, our architecture enters a regime where gravity-induced decoherence could be tested directly.