In 1879, Smith was asked by the LDS Church to become the president of the San Juan Mission of the church in southern Utah. In this capacity, he was asked to locate a suitable spot for a Mormon settlement on the San Juan River. Smith led the San Juan Expedition via the Hole in the Rock Trail, establishing the settlement of Bluff. Smith remained president of the San Juan Mission until 1882. In April 1880, Smith became a member of the LDS Church's Council of Fifty.
