Cooley remained with the Beaneaters for the following two seasons, hitting .289 in 1903. On June 20, 1904, Cooley hit for the cycle (a single, double, triple, and home run in the same game), becoming the second Beaneater to do so. Cooley finished the 1904 season with six total errors, five in the outfield and one at first base. Cooley's 70 RBIs were eighth most in the NL. After the season, in October 1904, he was selected off the Beaneater's waivers by the Detroit Tigers.