During the American Revolution, he served as ensign under is father, Col. Elias Dayton, in the Third New Jersey Regiment.
On January 1, 1777, he was commissioned as a lieutenant and served as paymaster. He served under Washington, fighting in the battles of Brandywine Creek and Germantown. He then remained with Washington at Valley Forge and helped push the British from their position in New Jersey into the safety of New York City. In October 1780, Jonathan Dayton and his uncle were captured by Loyalists, who held them captive for the winter releasing them the following year. He then served under his father again in the New Jersey Brigade. On March 30, 1780, at the age of 19, he was promoted to the rank of Captain and transferred to the 2nd New Jersey Regiment where he took part in the Battle of Yorktown. His pension records show that he served as Aide-De-Camp to General Sullivan on his expedition against the Indians from May 1 to November 30, 1779. On July 19, 1799, Jonathan Dayton was offered a commission as Major General in the Provisional United States Army, but declined.
After the war, Jonathan Dayton studied law. He divided his time between land speculation, law and politics. His land speculation efforts are how he ended owning land in what is now, Dayton, Ohio. He sat in the assembly in 1786-1787. He was chosen as a delegate to the Constitutional Convention after his father and his patron, Abraham Clark, declined to attend. Although objecting to some provisions of the Constitution, he signed it and was the youngest person to do so.