In Greeneville, Tennessee, October 1, 1862, Dr McDowell became Colonel of the 60th Regiment, when the regiment guarded military supplies and railroad bridges. He was among the eighteen officers and staff of the 60th Regiment who resigned before a court martial at winter quarters in Tullahoma, Tennessee. He along with the other officers were held responsible for companies of the 60th Regiment that returned to camp December 31, 1962, during the battle at Stone's River near Murfreesboro, Tennessee, when confused under heavy fire from federal troops protected by large, brick Cowan Farmhouse surrounded by outbuildings and picket fences, to fight again January 2, 1863. Officially, Joseph Alberto McDowell's April 22, 1863 resignation was due to chronic hemmorhoids.