He was appointed as AIK's manager on 10 November 2008 immediately following the end of the 2008 AIK campaign under Rikard Norling. For the two previous years he had served as manager of FC Väsby United, whom he first promoted from the third tier of Swedish football to the second tier Superettan. In 2008 Stahre led the team to the middle of the table despite having the youngest squad in the league.
Stahre is a national championship winning coach for men's junior after leading the AIK youth side to the title in 2004. He has also trained youth teams at Hammarby IF and Gröndals IK. On 26 April 2010 Panionios F.C. Panionios signed Stahre as the new manager. On 28 October 2010 Panionios F.C. announced the end of cooperation with Mikael Stahre.