In June 2016, Toppmöller became manager of F91 Dudelange, having taken them to the Group Stages of the UEFA Europa League for the first time in the club's history in 2018–19, campaign which F91 Dudelange have finished with one point following a draw in their last game against Real Betis. This feat made history in Luxembourg's football history, as Dudelange were not just the first team to have ever qualified in the group stages of any European competition, but they also managed to obtain a point. He joined Belgian outfit Virton following that season, having spent a brief stint with them before being released after just one season.[3]
On 20 July 2020, he was introduced as assistant coach to Julian Nagelsmann at RB Leipzig.[4] On 18 June 2021, he followed coach Nagelsmann to be his assistant at Bayern Munich.[5] On 24 March 2023, Nagelsmann was sacked by Bayern along with his assistant coaches including Toppmöller.[6]
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