He was detached from duty in April 1837 to mediate a conflict at Mobile Point, Alabama, over the proper delivery of contracted beef for the Creek Indians who were being rounded up and transported to their new lands in the West.

In 1838, he headed up the final preparations for the migration of the Cherokee Indians from western North Carolina and eastern Tennessee, the Trail of Tears.

Wilson was appointed to the post of military governor of that city in March 1847 and served in that capacity, with a few leaves of absences for sickness, until the U.S. Army pulled out of Mexico in July 1848.

Colonel Wilson however was on leave at the time the orders arrived and was in San Antonio temporarily commanding the Department of Texas through the summer of 1858.

He is rumored to have offered his services to fight for the Confederate States, but no evidence exists to suggest he was accepted or had any military role.