Microwave integrated quantum circuits with cap wafers and their methods of manufacture

In a general aspect, an integrated quantum circuit includes a first substrate and a second substrate. The first substrate includes a first surface and a recess formed in the first substrate along the first surface. The recess has a recess surface and is configured to enclose a quantum circuit element. The first substrate includes a first electrically-conductive layer disposed on the first surface and covering at least a portion of the recess surface. The first electrically-conductive layer includes a first superconducting material. The second substrate includes a second surface and a quantum circuit element. The second substrate includes a second electrically-conductive layer on the second surface that includes a second superconducting material. The first substrate is adjacent the second substrate to enclose the quantum circuit device within the recess. The first electrically-conductive layer of the first substrate is electrically-coupled to the second electrically-coupled layer of the second substrate.