Stöger became coach of coach of Austria Wien on 6 May 2005 together with Frank Schinkels till the end of the season. Stöger continued in the position until December 2005. In December he became sporting director. The following season did not start well and he was sacked in both positions. Stöger moved for 3 years to First Vienna FC, then Grazer AK and SC Wiener Neustadt. Then Stöger returned to Austria Wien on 30 May 2012, and won the Austrian championship with a record number of points.