Freund started his career at Stahl Brandenburg, coming through their youth system. He has said that the Stasi made an unsuccessful attempt to recruit him as an informer during his time at the club. In 1991, he was transferred to FC Schalke 04 and he established himself as an important midfield player. Schalke were forced to sell Freund due to financial reasons in 1993 to Borussia Dortmund where he stayed until 1998. During his time at Dortmund, he won the league twice in 1995 and 1996 and gained a Champions League medal in 1997, but was left out of the squad for the final altogether.