A few years later the outbreak of the Civil War brought Webster back into the service of the army. On June 1, 1861 he was appointed major in the U.S. Army Paymasters. In September he became chief of staff to Ulysses S. Grant. On February 1, 1862 Webster was appointed colonel of the 1st Illinois Light Artillery Regiment, but remained as Grant's chief of staff through the battles of Belmont, Fort Henry, Fort Donelson, and Shiloh.