When the American Civil War began in 1861, Philips chose to follow his home state of Georgia and the Confederate cause. On November 18 he was elected colonel of the 31st Georgia Infantry, assuming command of the regiment on the following day. Philips was then ordered to Savannah, Georgia, where it spent that winter. During the reorganization of the Confederate Army in the spring of 1862, Philips was not re-elected and resigned his commission on May 13. That same day Maj. Clement A. Evans was named colonel and replaced Philips in command of the 31st Georgia.