From 15 March 2004 on, Krüger was head coach of Eintracht Braunschweig and led the club back in the 2. Bundesliga in 2006. On 4 October 2006, Krüger was fired together with sporting director Wolfgang Loos by the Lower Saxon club. On 13 June 2007, Krüger was named as the new head coach of the Regionalliga relegated team 1. FC Saarbrücken, following the club's hiring of Wolfgang Loos in April 2007.
In January 2008, Krüger went back to Africa to coach Sudanese club Al-Merreikh, he led Al-Merreikh to win the Sudanese Premier League cup in November 2008 and the Sudan Cup in December 2008. Krüger signed on 21 September 2009 a contract as head coach with Alemannia Aachen and was just a half year later dismissed.
In the summer of 2010, he returned to the Sudanese club Al-Merreikh SC. In November 2010, he led the club to victory in the Sudanese Cup. After that he left the club.