In 1861, Wilson was a Union delegate to the Missouri Constitutional Convention (1861-63) called to determine the attitude on secession in 1861 and was elected vice president of the convention, later acting as president. He was appointed as a Unionist to the U.S. Senate to fill the vacancy caused by the expulsion of Waldo P. Johnson and served from January 17, 1862, to November 13, 1863, when a successor was elected. He engaged in agricultural pursuits and in 1870 he died in Marshall, Missouri. Interment was in Mount Mora Cemetery, St. Joseph, Missouri.