At the beginning of the 1896 season, Cooley continued to play for the Browns. However, after 40 games in which he had a .307 batting average, he was moved to the Philadelphia Phillies in exchange for Joe Sullivan, Tuck Turner, and an unknown sum of money. The Phillies, under manager Billy Nash, finished 62–68, eighth in the NL. Cooley remained with the Phillies in 1897, when he tied with Fred Tenney, George Van Haltren, and Gene DeMontreville for the MLB lead in at-bats. Cooley led his team in runs scored and stolen bases, and finished third, behind Ed Delahanty and Nap Lajoie, in hits. The following two seasons, playing for Philadelphia, he hit .312 in 1898 and .276 in 1899, before he was purchased by the Pittsburgh Pirates for US$1,000 in April 1900. In his only season with the Pirates, Cooley recorded a batting average of .201, the worst of his career. He also compiled 30 runs, 50 hits, and 22 RBI.