After the war, Atkinson led two expeditions to the Yellowstone River in 1819 and 1825. He was appointed brevet brigadier general and was in overall command of U.S. forces during the Black Hawk War. Although he delivered the final blow to the Black Hawk Indians at the Battle of Bad Axe, Atkinson was criticized for mishandling the operations of the war and his reputation did not prosper as did those of his subordinates Zachary Taylor and Henry Dodge.
Atkinson later superintended removal of the Winnebago to Iowa. Jefferson Barracks (near St. Louis) and Fort Leavenworth were begun under his direction. He spent the remainder of his career stationed at Jefferson Barracks.
He married Mary Ann Bullitt on January 16, 1826 they had a son Edward Graham Atkinson.