Nichols had his first losing season in 1900, when he went 13–16. He improved to 19–16 the following year. After the 1901 season, Nichols purchased an interest in a minor league franchise in Kansas City. He left the Beaneaters to manage and pitch for the Kansas City club, where he won a total of 48 games in 1902 and 1903. After a two-year hiatus from the major leagues, Nichols returned to the 20-win plateau for the 11th and final time in his career in 1904 for a new team, the St. Louis Cardinals. The Philadelphia Phillies picked him up off waivers in 1905, and he finished his career with them in 1906, playing his final game on May 18, 1906.