After finishing his playing career, he began working as a coach for the Rapid amateurs, continuing his association with the club until 2006.

On 11 November 2006, after sustaining criticism for negotiating TV punditry contracts while allowing his duties at Rapid to wane, he left the club.

In the summer of 2007, he began work as a trainer with Wiener Sportclub with his contract running until the end of June 2008.

[1] His squad number, 5, was retired by Rapid Wien until the 2011 season as a mark of respect for Schöttel's playing career.

In December 2009, Schöttel was appointed as manager to the Austrian Bundesliga club SC Wiener Neustadt.