Mehnert began his career with his hometown club, Borussia Dortmund, and progressed through the reserve team, being promoted to the first-team squad of the then-European champions in 1997. He made his debut in the second leg of the UEFA Super Cup against Barcelona, replacing Steffen Freund as a 20th-minute substitute, and made three appearances in the Bundesliga, and one in the Champions League, against Sparta Prague.