 When Erwin Koeman quit as head coach of FC Utrecht in October 2011, Alflen was assigned as assistant coach of Jan Wouters for the first team of FC Utrecht.He became head coach after Wouters left the club in June 2014.On 25 March 2015 FC Utrecht said that coach Alflen and his advisor Co Adriaanse would step down from their roles with the Dutch club at the end of the season.