Promoted to the rank of Major (United States) soon after returning to duty, Wilson was severely wounded, shot three times during the Battle of Chickamauga. After recuperating in Wisconsin (during which time he married Mary Madson, 1843–1903), Wilson returned in November 1863 as acting commanding officer of the Scandinavian Regiment during the Battle of Rocky Face Ridge, Resaca and Pickett's Mill (during which the regiment suffered particularly heavy casualties) before turning command over to Col. Ole Johnson in July 1864. Wilson remained with the regiment, serving in an additional 26 military engagements, until the war's end in 1865.