He was brought back to Silkeborg IF as manager in October 2001. He managed the club for nine months, and succeeded in avoiding relegation to the Danish 1st Division. In September 2005, he was appointed manager of SønderjyskE where he stayed for eight months until he was fired.
Morten is currently a football expert for Kanal 6 in Denmark which allows him to travel in England and Spain commenting upon live matches. He is also coach in Lyseng IF youth department (U17 and U19 boys)