The second season of Mystery Road: Origin was filmed in Pemberton, Western Australia's Southwest region. Filming took place in various locations across Pemberton, including Yeagarup, Pemberton District High School, Pemberton Caravan Park, Pemberton Pool, and the surrounding Deanmill area. This season continued to delve into the early years of Detective Jay Swan and brought a new Western Australian director, Jub Clerc, to the franchise. The production in Pemberton followed earlier seasons which were filmed in other parts of Western Australia such as Kalgoorlie, the Kimberley, Broome, and the Dampier Peninsula.