Active in the secessionist movements in his hometown of St. Louis, Missouri, in 1861, Greene worked with Governor Claiborne Jackson to promote the Southern cause. He received a commission as a colonel. In the Spring of 1862, he took command of the Confederate 7th District in Missouri. He led a force at the Battle of Pea Ridge in March 1862. He later raised the 3rd Missouri Cavalry, of which he was appointed colonel. In June 1864, he commanded a division in a delay of the Union advance at Old River Lake, Arkansas. He continued to serve as the colonel of the 3rd Missouri Cavalry until the end of the war.
