The Indigenous population on the Crow Creek reservation was expelled in 1866. Williamson went with them to Niobrara, Nebraska. He remained in Niobrara until March 1869, when he became a missionary to the Yankton Sioux Tribe at Yankton Agency in South Dakota. He remained in South Dakota until his death. He reportedly oversaw the construction of 39 churches in South Dakota, which were organized into the Dakota Indian Presbytery.