A method of forming a superconductor interconnect structure is disclosed. The method includes 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 includes depositing a superconducting metal in the interconnect opening, by performing a series of superconducting deposition and cooling processes to maintain a chamber temperature at or below a predetermined temperature until the superconducting metal has a desired thickness, to form a superconducting element in the superconductor interconnect structure.