In 1999, he worked one year lower league team VfV Hildesheim, before signing a contract as assistant coach of Erich Rutemöller at F.C.
In 1998, he returned to Germany and was named head coach of Kickers Emden and later took the same job at the second team of VfL Wolfsburg.
From 15 March 2004 on, Krüger was head coach of Eintracht Braunschweig and led the club back in the 2.
On 4 October 2006, Krüger was fired together with sporting director Wolfgang Loos by the Lower Saxon club.
[4][5] In 2013, he returned to Al-Merreikh in Sudan, but was fired after a loss against Uganda's Kampala City Council FC in the CAF Champions League in February 2014.