In 1861, Nelson was sent to Kentucky as a recruiter. In September 1861, he was promoted to brigadier general. In command of a division in the Army of the Ohio, Nelson led his forces at the battles of Shiloh, Corinth, and Chattanooga. He was promoted to major general in July 1862. Nelson was detached from the Army of the Ohio and sent to Nashville, Tennessee, and into Kentucky, in pursuit of the retreating Confederate forces. In August 1862, he was defeated at Richmond, Kentucky. During this fight, Nelson was wounded and a month later, he was shot by a disgruntled fellow officer during an argument.