test equipment to apply an alternating bias to a heated tunnel barrier, giant increases in the room temperature resistance, greater than 70%, can be achieved. The rate of resistance change is shown to be strongly temperature-dependent, and is independent of junction size in the sub-micron regime. In order to measure their tunneling properties at mK temperatures, we characterized transmon qubit junctions treated with this alternating-bias assisted annealing (ABAA) technique. The measured frequencies follow the Ambegaokar-Baratoff relation between the shifted resistance and critical current. Further, these studies show a reduction of junction-contributed loss on the order of ≈2×10−6, along with a significant reduction in resonant- and off-resonant-two level system defects when compared to untreated samples. Imaging with high-resolution TEM shows that the barrier is still predominantly amorphous with a more uniform distribution of aluminum coordination across the barrier relative to untreated junctions. This new approach is expected to be widely applicable to a broad range of devices that rely on amorphous aluminum oxide, as well as the many other metal-insulator-metal structures used in modern electronics.