He was made a brevet major and a brevet lieutenant colonel on 1 August 1864 for his "gallant service" at the Battles of North Anna and Bethesda Church, respectively. McKibbin was imprisoned successively at Libby Prison, at Camp Oglethorpe in Macon, Georgia, and at Camp Sorghum in Charleston, South Carolina until paroled in October, but remained at Camp Parole until exchanged in December. After serving with the 14th Infantry in New York until February 1865, McKibbin remained on recruiting duty in New York until April; he was promoted to brevet colonel and brevet brigadier general (both Volunteer and Regular Army) on 13 March 1865 for "gallant and meritorious service" during the war. McKibbin became the Colonel of the 214th Pennsylvania Infantry on 5 April and led it in the Army of the Shenandoah and in the garrison of Washington, D.C. until it was mustered out on 30 April 1866.