Fred Clarke, manager of the Pittsburgh Pirates, had Lobert try every infield position except for first base. He had five appearances in the fall of the 1903 season. He had three errors and only hit 1 ball of 13 at-bats. The hit was during a game against the New York Giants with Joe McGinnity as pitcher, and Lobert bunted for a single. In 1904, The Pirates sold him to Des Moines, Iowa which was part of the Western League. He would go on to play 143 games that season. Lobert batted .264 and stole 37 bases. When the team came under new ownership in 1905, Lobert was offered a contract with a significant pay put, he jumped teams with the added advantage of playing closer to home. He would play for Johnson as part of the Tri-State League, where he played 115 games, batted .337, and stole 31 bases. That same season the Chicago Cubs would buy Lobert from Johnson, and he would bat .196 in his 14 games. He was traded once again before the start of the 1906 season; this time to the Cincinnati Reds where he would bat .310 and steal 20 bases in his 79 games. 35 of his games were at third base, 31 were as a shortstop, and 10 were played at second base. He replaced Tommy Corcoran as the everyday shortstop in 1907. In the middle of the 1908 season, Lobert made his career changing move as third baseman.