A method is provided of forming a superconductor interconnect structure. The method comprises forming a dielectric layer overlying a substrate, forming an interconnect opening in the dielectric layer, and moving the substrate to a deposition chamber. The method further comprises performing a cleaning process on the top surface of the dielectric layer and in the interconnect opening while in the deposition chamber, and depositing a superconducting metal in the interconnect opening while in the deposition chamber to form a superconducting element in the superconductor interconnect structure.