A quartz Bulk Acoustic Wave resonator is designed to coherently trap phonons in such a way that they are well confined and immune to suspension losses so they exhibit extremely high acoustic Q-factors at low temperature, with Q × f products of order 1018 Hz. In this work we couple such a resonator to a Superconducting Quantum Interference Device (SQUID) amplifier and investigate effects in the strong signal regime. Both parallel and series connection topologies of the system are investigated. The study reveals significant non-Duffing response that is associated with the nonlinear characteristics of Josephson junctions. The nonlinearity provides quasi-periodic structure of the spectrum in both incident power and frequency. The result gives an insight into the open loop behaviour of a future Cryogenic Quartz Oscillator in the strong signal regime.