Maffitt joined the C.S. Navy with his cousin, E. M. Anderson, in 1861. Both served together at the Savannah Station until they were transferred to the CSS Alabama. He was in charge of two 32-pounder guns in Wilson’s division. After the Alabama was sunk–he was rescued by the Deerhound. In December 1864 he was captured on a English steamer docked at Portland, Maine, and was incarcerated at Fort Warren  until 1866. After the war he settled in Wilmington, NC, where he died in 1886.