The basis for superconducting electronics is the Josephson junction, a thin insulating barrier that separates two superconducting leads and
thereby behaves as a tunneling barrier. These junctions are the non-linear circuit element inside superconducting quantum interference
devices, low temperature microwave electronics, and superconducting quantum computers. The width of this barrier can be as thin as two nanometers and the electronic properties of such junctions are strongly dependent on the morphology of the barrier, both at the interfaces of the superconducting leads and within the metal oxide itself. Using a range of computational techniques we analyse how the junctions are formed and how their electrical response depends on the junction microstructure.Our results provide new insights into the influence of fabrication conditions on the electrical response of metal-oxide barriers and the resulting performance of quantum technologies constructed from them.