Apprenticed in a shipyard, during the American Revolutionary War, he saw combat in the battles of Trenton and Princeton and later served at sea.

In the decades that followed the war, he was a successful merchant in Charleston, South Carolina, and in Philadelphia.

He was elected as a Republican to the United States House of Representatives in 1800 and was offered the office of Secretary of the Navy in 1801, but declined and remained in Congress to the end of his term in 1803.

In late 1814, near the end of his term, he made recommendations on the reorganization of the Navy Department.

From May 1813 to February 1814, Jones also served as acting Secretary of the Treasury and in 1816 was appointed President of the Second Bank of the United States.