In light of his success, Toppmöller became coach of Eintracht Frankfurt, with whom he had a very successful start. But after failures with the squad relationship and resultantly missing the championship he was dismissed on 10 April 1994. Toppmöller then joined VfL Bochum on 9 November 1994, with whom in the 1997/98 season reached the last sixteen of the UEFA cup. On 30 June 1999 Toppmöller left his position as coach of VfL Bochum, but was eventually dismissed on 29 November 2000.
From 1 July 2001 Toppmöller was coach with Bayer 04 Leverkusen, whom in his first season led to the final of the UEFA Champions League, as well as second place in federal league and the German cup final. Toppmöller was resultantly declared by German sports journalists as "football coach of the year" for 2002. However, in the following season Leverkusen performed poorly, and in light of a poor league position which could have led to relegation, Toppmöller was sacked on 16 February 2003.
Toppmöller became coach of Hamburger SV on 23 October 2003. However, after the team fell to last place in the league, and Toppmöller used strange tactics, formations and out of position players (such as midfielderSergej Barbarez in defence), he was sacked on 17 October 2004.