In 1898, when the Spiders' owners purchased the St. Louis Browns franchise, McAleer opted to stay in Cleveland, taking a brief hiatus from baseball until the Cleveland Blues franchise joined the newly formed American League (AL). During his two-year absence, the Spiders lost many of their more experienced players. In 1899, the team won 20 games and lost 134, which is still percentage-wise the worst season record in Major League history. As baseball historian Bill James noted, the Spiders were forced to cancel home games due to poor attendance and "turned the last two months of the season into a long road trip". After a full year out of baseball in 1899, McAleer was back in a Cleveland uniform in 1900, in a new league, as player-manager of the Cleveland Lake Shores of the fledgling American League, then a minor league. McAleer's subsequent career as a major league manager (1901–11) overlapped with his playing career (1882–1907). Although he did not play professionally between 1903 and 1906, McAleer played in his last Major League game on July 8, 1907.