During the 1780s, Walton devoted himself almost exclusively to Georgia state politics. He served not only as chief justice but also as a commissioner to negotiate a treaty with the Cherokee Indians (1783), a member of the Augusta Board of Commissioners (1784 and 1785), and a commissioner to settle the border dispute between South Carolina and Georgia (1786). He was elected as a delegate to the Constitutional Convention in 1787 but declined, as his commitments at the state level occupied his time to the exclusion of all else. In 1789 he was a presidential elector and served at the state convention to adopt a new constitution. Walton was elected to a second term as governor in 1789 and served for one year. During his term, Georgians adopted the new state constitution, moved the capital to Augusta (where Walton himself had moved in the 1780s), and concentrated on settling the western frontier. After completing his tenure as governor, Walton served as a judge of the superior court from 1790 until his death. He also filled the unexpired term of James Jackson in the U.S. Senate in 1795–1796. He was a founder and trustee of the Academy of Richmond County in Augusta and of Franklin College (now the University of Georgia) in Athens.