Jones was born in Newport in the Colony of Rhode Island and Providence Plantations,[1] into a family of Welsh origin.

His grandfather Thomas Jones (1691–1740) was born in Wales and settled in the Colony of Rhode Island and Providence Plantations.

[2] In January 1776, at age 23, Jones was commissioned as Lieutenant in Babcock's/Lippitt's Regiment, which was raised in Rhode Island.

[2] On March 4, 1778, Jones was commissioned as captain of Marines on board the sloop USS Providence.

By right of his service in the Continental Army and Marine Corps, Jones became an Original Member of the Rhode Island Society of the Cincinnati.

[4] Jones was a Federalist and won the gubernatorial election against incumbent James Fenner in 1811 by just a few hundred votes.

[2] Jones nephew, William Henry Allen, was an American naval officer during the War of 1812.