Jonathan was born in 1646, in Saybrook, Connecticut. His parents were Thomas and Mary Conway Tracy. He was one of the founders of Preston, New London, Connecticut. The first recorded Town Meeting took place on 30 March 1687. The first order of business was to choose a Recorder [town clerk]. Jonathan Tracy was chosen for this position. No other officials were appointed at the first meeting. The business that followed dealt with the granting of land; thus the need for the Recorder being the first official chosen. The records of Preston say that Jonathan Tracy married Mary Griswold on July 11, 1672. Since the first recorded town meeting took place in 1687 and Jonathan was chosen to be town clerk, he might have decided to put the record of his own marriage in the records of Preston, even though it did not occur there. They were married in Lisbon, New London County, in the Newent Congregational Church. The births of their first five children also occured before 1687, but are also found in the records of Preston. Those children were probably also born in Lisbon.

Jonathan was Commissioned Lt. of the Preston militia, May 1690. Jonathan was Selectman of Preston in 1698, and served as Town Clerk until his death. Colony law required that every town have an 'ordinary'. This term was used very early but changed to the more familiar 'tavern'. Jonathan Tracy was the first Ordinary Keeper. From the town records, 1698 jenewary 25: jonathan Tracy was chosen ordinary keeper. Jonathan and Mary had at least nine children. Three of their sons married daughters of John and Mary (Wattell) Parish: Christopher married Lydia Parish, David married Sarah Parish, and Francis married Elizabeth Parish. Jonathan's will, dated Nov. 1711, mentions wife Mary, sons David and Samuel of Preston, and daughter Mary, wife of Benjamin Parrish. Jonathan signed a deed on November 29 and his will was proved on December 24, 1711. His place of burial is unknown.