When a member of the council in 1787, Kilty introduced a resolution proposing to change the method of compensation for the state's "Agent for special purposes." The motion lost on a tie vote, but Kilty exercised his privilege of having an opinion in support of the resolution filed with the council records. His opinion was published as "John Kilty on the Agent's Salary," in the March 1911 issue of the Maryland Historical Magazine, pp. 357-65. Kilty had also begun work on a history of Maryland (a project to which he alludes in The Land-holder's Assistant), but that project remained unfinished when he died.

John Kilty married Catherine (Kitty) Quynn on 9 May 1792. Catherine Kilty was the daughter of Allen Quynn (c.1726-1803) and his wife Elizabeth. Quynn was a shoemaker, or cordwainer, who had attained considerable success in Annapolis, as a land developer, entrepreneur, tanyard owner, and ferry operator. He represented Annapolis in the lower house from 1777 to 1802 and held local offices as coroner, councilman, constable, alderman, vestryman of St. Anne's, and justice of the peace. The Kiltys had at least seven children (William, prob. 1794-?), Richard, George (c.1805-1825), Augustus (1807-1879), Ellen, Mary, and Elizabeth. An Annapolis acquaintance of the Kiltys, diarist William Faris, recorded at the time of their marriage that "Capt. Kilty married Kitty Quynn and the Town Talked that he should have marryed her sooner as she's with child." He then noted the child's birth on 11 or 12 August of the same year: "either last night or this morning Kitte Kilty was delivered of a daughter. I think they have not been Idel, being only marryed the 9th of May last." This daughter may well have been Ellen, the Kiltys thus naming their first-born daughter after her paternal grandmother. Faris also noted the (presumed) birth of William on 3 June 1794: "Capt. John Kelty's wife's Brought to bed of a fine Boy about 8 oclock this morning."

When Allen Quynn died in 1803, the Kiltys moved into one of his houses on West Street in Annapolis. John Kilty and his brother-in-law, Col. John Gassaway, husband of Mary (Polly) Quynn were named as executors. Each received a one-quarter share of the estate with the remaining shares going to their brother-in-law John Quynn and the children of Allen Quynn, Jr. Quynn left an estate whose value was at least $13,000 in personal property, four lots in Annapolis, a tanyard, and about 800 acres in Anne Arundel County. Settlement of the estate required several chancery court cases to resolve claims and obtain permission to sell the real estate. Kilty advertised Quynn's house for rent in April 1804, but it appears that rather than renting the home, the Kiltys themselves lived there, and the property was not sold until 1813, two years after Kilty's death.

John Kilty died on 27 May 1811, "after a long and severe illness," according to the 29 May Maryland Gazette. The 6 June 1811 issue of the Federal Gazette and Baltimore Daily Advertiser marked his death as that of "Another Revolutionary Hero Gone." The American, published on 30 May, wrote that "His demise is truly an irreparable loss to a numerous family, to the State, and to society in general. In our revolutionary contest he shared the dangers of the field and reaped a portion of his reward in British dungeons. He has spent much of his time usefully in literary pursuits. Whether we regard him as a soldier or a civilian, his talents were of a higher order eminent at the bar [although John Kilty was not a lawyer] and brave in the field, he won the affection and commanded the respect of all who knew him." Kilty is presumably buried in St. Anne's Cemetery in Annapolis, where a single marker records both his death and that of his brother William, a surgeon (during the Revolution) and lawyer, who compiled The Laws of Maryland(Annapolis, 1799) and served as chancellor from 1806 until he died in 1821.