A number of Dr. Prescott's family were Patriots in the American Revolution. His nephew Samuel road with Paul Revere. Samuel eventually was taken prisoner to Halifax where he is reported to have died during the war. Jonathan named one of his son's after his nephew Samuel and he is buried in Old Burying Ground (Halifax, Nova Scotia). Jonathan's son Joseph joined the Continental Army, fought at Fort Ticonderoga and was a founding member of the Society of the Cincinnati. Another of Dr. Prescott's sons John fought in the Battle of Lexington. His other son was Charles Ramage Prescott.