On March 2, 1863, McIntosh was promoted to major and given command of an artillery battalion. He commanded his battalion at the Battle of Chancellorsville, and at the Gettysburg, Bristoe Station, and the Mine Run battles. McIntosh was promoted to lieutenant-colonel in February 1864 and commanded his battalion in the Overland Campaign, including the Battle of the Wilderness. He fought along the siege lines at the Siege of Petersburg and was slightly wounded at the Battle of the Crater. Shortly thereafter he was wounded at the Battle of Weldon Railroad.