Conway had his best season in 1888. He appeared in 45 games for Detroit and pitched 43 complete games and 391 innings. He finished the season with a record of 30 wins and 14 losses, and his winning percentage (.682) was the second highest in the National League. It would be 80 years before another Detroit pitcher would win 30 games, when Denny McLain did it for the Detroit Tigers in 1968. At the end of the 1888 season, the Detroit franchise disbanded. Conway traveled to New York in November 1888 to offer his services to other clubs at a meeting of the National League. William A. Nimick, the president of the Pittsburgh Alleghenys, offered Conway a salary of $3,500 per year, but Conway refused to sign unless he was paid $4,000 per year. Conway indicated that he preferred to play for the Boston Beaneaters, where four of his Detroit teammates known as the "Big Four" (Dan Brouthers, Hardy Richardson, Jack Rowe, and Deacon White) had signed. However, Conway was told that, following the breakup of the Detroit franchise, he "had been allocated to Pittburg." After talking with Fred Dunlap, a former teammate who had played for the Alleghenies in 1888, Conway ultimately agreed to sign a two-year contract for $3,500 per year. During the 1889 season, Conway appeared in only three games for the Alleghenies. Though he won two of the three games, his earned run average soared to 4.91 – more than double his 1888 earned run average of 2.26. Conway appeared in his final Major League game on May 9, 1889. He was suspended without pay by the Alleghenies who claimed that he was not in condition to play. It was reported in the press that Conway had "snapped a cord in his arm," and that his "anterior detroid muscle was out of whack." The Alleghenies' suspension of Conway without pay following his injury sparked an early controversy over players' rights. In August 1889, newspaper accounts noted: "Pete Conway will be backed by the brotherhood in a suit against the Pittsburg club this fall. He was laid off without pay, but reports for duty, every day." In September 1899, Conway was reported to be using electricity on his arm to offset the effect of the injury. In March 1890, Conway signed with the Brooklyn franchise in the newly formed Players' League. By late June, newspapers reported that he had been with the team for two months, but had not yet appeared in a game.