We propose a scheme involving a Cooper pair transistor (CPT) embedded in a superconducting microwave cavity, where the CPT serves as a charge tunable quantum inductor to facilitate ultra-strong coupling between photons in the cavity and a nano- to meso-scale mechanical resonator. The mechanical resonator is capacitively coupled to the CPT, such that mechanical displacements of the resonator cause a shift in the CPT inductance and hence the cavitys resonant frequency. The amplification provided by the CPT is sufficient for the zero point motion of the mechanical resonator alone to cause a significant change in the cavity resonance. Conversely, a single photon in the cavity causes a shift in the mechanical resonator position on the order of its zero point motion. As a result, the cavity-Cooper pair transistor (cCPT) coupled to a mechanical resonator will be able to access a regime in which single photons can affect single phonons and vice versa. Realizing this ultra-strong coupling regime will facilitate the creation of non-classical states of the mechanical resonator, as well as the means to accurately characterize such states by measuring the cavity photon field.