In March 1862, President Lincoln organized the Army of the Potomac into corps, and Heintzelman received the III Corps of the Army of the Potomac in the Peninsula Campaign. His corps played a prominent role in the Siege of Yorktown where Heintzelman and division commander Fitz John Porter were among the first to use the Union Army Balloon Corps. The corps bore the brunt of the fighting at Williamsburg and saw significant action at Fair Oaks, Oak Grove, and Glendale. His corps was temporarily attached to the Army of Virginia and took part in the Second Battle of Bull Run. He was commissioned as a brevet brigadier general in the regular army for the battle of Fair Oaks and a major general of volunteers for the battle of Williamsburg. At the Battle of Glendale, Heintzelman was bruised in the wrist by a spent bullet and was unable to use his left arm for a few weeks. After the Seven Days Battles, he was promoted to major general of volunteers to rank from May 5. His popularity and confidence in the army were eclipsed by the aggressive nature of his subordinate division commanders Joseph Hooker and Philip Kearny, and he did not display any notable leadership or tactical prowess in either the Peninsula Campaign or Second Bull Run, although following the Union retreat from Gaines Mill, he was one of three corps commanders to advocate launching a counterattack against the Army of Northern Virginia.