Jacobs became new manager of FC Copenhagen in June 2012 following Carsten V. Jensen's resignation.[2] His first season as manager of the club was a success and he led the club to the Danish Superliga-title in the 2012–13 season.[3] On 21 August 2013, he was sacked as manager of FC Copenhagen as he failed to win in his first five games in the league.[4]
On 14 October 2013, Jacobs was appointed manager of Valenciennes FC.[5] He failed to secure the team from relegation following the 2013–14 Ligue 1 and he therefore left the club in July 2014.[6]