After retirement, Sammer became head coach of Borussia Dortmund on 1 July 2000. Sammer led Borussia Dortmund to another Bundesliga title in 2002. His team reached the 2001–02 UEFA Cup final the same year but lost 2–3 against Feyenoord. Sammer was sacked at the end of the 2003–04 season after Dortmund finished in sixth place.