After the British capture of Charleston in 1780, Clarke and his Georgians participated in the guerilla campaign against the British and their supporters in the South Carolina backcountry. He was one of three American commanders at the Battle of Musgrove’s Mill, during which he was wounded. Clarke would go on to serve in Georgia’s legislature from 1781 to 1790 and in the 1789 state constitutional convention. He also continued to lead militia forces against Native Americans. In early 1794, Clarke accepted a French commission as a major general and planned to mount an attack on the Spanish colony of Florida.