Jonathan Prescott was suspected of being an American Patriot sympathizer given that, after the initial hostile engagement, he reportedly allowed Captain Noah Stoddard to bury his dead and then had tea with him the day before Stoddard orchestrated the raid on Lunenburg. People were also suspicious of Prescott's allegiance, because a number of Dr. Prescott's family were Patriots in the American Revolution; his nephew Samuel had ridden 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 sons after Samuel and he is buried at the Old Burying Ground in Halifax. 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.