Phelps was an aide-de-camp on the staff of Brigadier GeneralEugene Asa Carr from September 1862 to April 1864.[1] He was promoted to first lieutenant in the regular army on October 1, 1863.[1] In late 1862, while recovering from malaria, he organized the 2nd Arkansas Cavalry Regiment (Union). He was appointed colonel of the 2nd Arkansas Cavalry (Union) on March 18, 1864.[1][2] Phelps served as commander of Brigade 1 of the Cavalry Corps of the Military Division of West Mississippi from April 1865 to June 17, 1865; commander of Brigade 2 of the Cavalry Corps of the Military District of West Mississippi from June 17, 1865 to July 14, 1865 and of the Cavalry Division of the Military District of West Mississippi from July 14, 1865 until he was mustered out of the volunteer service.[1]
Phelps was mustered out of the volunteers on August 20, 1865 and resigned his commission in the regular army on September 28, 1865.[1] He received brevet appointments of captain, for the Missouri Campaign, major and colonel in the regular army to rank from March 13, 1865.[1]
After the war, Phelps became a farmer and a miner. He later moved to Tacoma, Washington. John Elisha Phelps died at Pasadena, California on September 17, 1921.[1] He was buried at Hazelwood Cemetery, Springfield, Missouri.[1]