In 1969, Stein began his professional baseball career in the St. Louis Cardinals minor league organization. The Cardinals assigned him to the Tulsa Oilers, who were their Triple-A affiliates at the time. With the Oilers, Stein batted .295 with 24 runs scored, 54 hits, 11 doubles, five triples, one home run, and 20 runs batted in (RBIs) in 62 games played. Defensively, Stein played 31 games at second base, 14 games at third base, and five games at shortstop. During the 1970 season, the Cardinals assigned Stein to the Double-A level to play with the Arkansas Travelers of the Texas League. In 114 games played that year, he batted .289 with 124 hits, 21 doubles, two triples, and eight home runs. In the field, Stein played second base and outfield. In 1971, Stein was promoted to the Triple-A level. He spent the entire season with the Tulsa Oilers, where he batted .272 with 50 runs scored, 106 hits, 106 hits, 22 doubles, four triples, eight home runs, and 67 RBIs in 103 games played. Stein pitched a game that season, after Tulsa's starting pitcher was ejected from the game after throwing the ball at the umpire. In six innings, he gave-up eight hits, and three runs (all earned). He played the majority of the season in the outfield, but also spent limited time at third base, first base, and shortstop.