Returning to duty the following spring, Ames was part of the defenses of Washington, D.C. He then fought in the Peninsular Campaign, and saw action at the Battle of Yorktown from April 5 to May 4, the Battle of Gaines' Mill on June 27, and the Battle of Malvern Hill that July. Ames was commended for his conduct at Malvern Hill by Col. Henry J. Hunt, chief of the artillery of the Army of the Potomac, and he received a brevet promotion to lieutenant colonel on July 1.