In November 1861 Philips was elected colonel of the 31st Georgia Infantry. He went to Virginia with this unit but quickly resigned to return to the militia. He was given the rank of brigadier general in command of a brigade of the Georgia Militia with the Army of the Tennessee, and, later, the Department of South Carolina. Philips led them through the Atlanta campaign but remained in the Department of South Carolina when the Army of the Tennessee went west. In November 1864 his force was ordered from Macon to Augusta to protect an armory; however, he ran into Union troops. At the Battle of Griswoldville, Philips was forced to withdraw from the field in the face of a well-fortified Union defensive. He served in the continued operations against the Union army in Georgia until the end of the war.
