When Governor Wright was forced out of Georgia in 1776, Jones and other revolutionaries assumed control of the colony. He helped write Georgia's 1777 state constitution and was elected Speaker of the new House of Assembly. The British recaptured Savannah in 1778, however, and Jones fled to Charleston, South Carolina. There he practiced medicine until, in 1780, the British also captured Charleston. He was held as a prisoner in St. Augustine, Florida, until he was exchanged in 1781. His first available transportation took him to Philadelphia, Pennsylvania, where he was appointed as a delegate to Congress.