Voltage-tunable hybrid superconductor-semiconductor Josephson junctions are promising building blocks for low-loss frequency-tunable quantum devices such as qubits and resonator couplers. The realization of hybrid devices in group IV semiconductors such as Ge is of particular interest due to higher scalability and low dielectric loss at microwave frequencies. However, inducing superconductivity in Ge via proximity effect has been proven to be challenging because of large interfacial energy barriers and defect densities. Here, we utilize ultrahigh vacuum evaporation to deposit high-quality Nb layers on Ge (001) substrates. Through various thermal cycling schemes, we tune the interface structures. Through X-ray photoelectron spectroscopy and femtosecond ultraviolet photoelectron spectroscopy we determine the impact the thermal cycling has on the band alignment and chemical composition of the interface. This is complemented by cryogenic measurements of interface losses for the Nb/Ge heterostructures as thin films and as coplanar waveguide resonators (at microwave frequencies).