Troy concluded his major league career as a member of the 1885 Metropolitans. He appeared in 45 games that year, including 42 at second base. His batting average dipped to .220 with three doubles, three triples, two home runs and 12 RBIs. Troy's last major league game was on July 9, 1885. Troy continued playing professional baseball in the minor leagues through the 1888 season, including stints with the Scranton Indians (39 games, 1886), Binghamton Crickets (36 games, 1886), New Haven Blues (55 games, 1887), Manchester Farmers (37 games, 1887), and Troy Trojans (62 games, 1888). Troy was managed in 1888 by Ted Sullivan, who frowned on Troy's consumption of alcoholic beverages. Troy agreed voluntarily to abstain from drinking as a condition for playing on the manager's team, but was unhappy with the restriction. Finally, in a home game during the 1888 season, Troy promised that, if Sullivan went to the bar under the grandstand and brought him a beer, Troy would "clear the bases." Sullivan complied, and Troy walked to the plate saying, "The 'Old Dash' is back." Troy hit the ball off the center field fence for an inside-the-park home run to win the game. Sullivan later recalled, "After that I never stopped my old friend, John Troy, from taking his glass of beer." Sullivan further recalled that no player impressed him more than Troy for the "natural way he picked up ground balls", as "a man of principle", and for his "originality, good humor and clean language in the style of coaching." As a New York native who played for the Gothams/Giants in their first season in New York, Troy was fondly remembered by New Yorkers. From approximately 1889 to 1900, and with the exception of the 1894 season when he lost his license after an attack on a grandstand gatekeeper, Troy operated the beer concession, sometimes referenced as a saloon or bar, at the Polo Grounds in New York. According to one account published in 1893, patrons sometimes "paid more attention to 'Dasher' Troy's emporium than they did to the game." In September 1900, he opened a café in his old home neighborhood at Tenth Avenue and Thirty-Ninth Street. Troy was married to Mary E. Flanagan in approximately 1890. By 1900, Troy was living with Mary in Manhattan and was employed as a liquor dealer.