Jonathan was born in Mile Square, Westchester County, New York around 1745, the son of Jonathan & Abigail Archer. Jonathan's wife was Mary Ann, her last name was possibly Smith. They had seven children. They moved to Yorktown Heights and before 1775, to Monroe, Orange County, New York, because Jonathan appeared on the assessment roll in that County in that year. He may have moved with his brother-in-law Jonas Garretson. During the War of the Revolution Jonathan served as an enlisted man in the 4th Regiment of Orange County Militia, Colonel John Hathorn commanding. In the 1790 Federal census for New York, he is listed at New Cornwall Town as head of a family consisting, in addition to himself and wife, of one male upwards of sixteen years of age, four under sixteen and two females (Miriam and Abigail) together with three slaves (p. 145). Ten years later he is reported with his wife in the census at the Town of Minisink, Orange County, New York. There he is listed as the head of a family of seven as follows: one male under ten years, one between ten and sixteen, two between sixteen and twenty-six, and one between twenty-six and forty-five, together with two females, one between ten and sixteen (Abigail) and the other between sixteen and twenty-six (Miriam) (NYGBR, vol. 64, p. 291). In the last mentioned census the parent's ages are given as over forty-five years.

Jonathan wrote his will on April 29, 1816 but it wasn't probated until May 10, 1821, in Goshen, New York (Orange County Wills, Liber F, p. 398). In the will, he named his wife Mary Ann, sons Jonathan, Caleb, James, John & William, daughters Elizabeth, Abigail & Miriam, grandchilden Jefferson Archer & his brothers & sisters. The executors were John Archer & John McGarrah. The witnesses were Samuel VanDuzer, John Brooks & Alexender McElroy. When the will was probated in 1821, his daughter Elizabeth and son William had died.