Cheatham was promoted to major general, on March 10, 1862, and was appointed commander of the 2nd Division, First Corps, Army of Mississippi. He led his division at the Battle of Shiloh and was wounded, although it is unclear whether this occurred on April 6 or April 7, 1862. General Braxton Bragg became commander of the Army (soon to be designated the Army of Tennessee) and Cheatham served under him at Perryville and Stones River. At the latter battle, Cheatham performed sluggishly, ordering piecemeal assaults; observers claimed he had been drinking heavily and was unable to command his units effectively. However, Pvt. Sam Watkins, author of "Company Aytch", claims to have personally witnessed Cheatham leading a charge on the Wilkerson Turnpike during the battle, indicating that he performed gallantly during that part of the battle, at least.