Innauer retired from competitions in 1980 due to an ankle injury. In 1987, he graduated from the University of Graz with a degree in philosophy, psychology, and sports science. His thesis was on the sociology of ski jumping. Between 1987 and 1989, he was a ski jumper and ski jumping coach. In 1989–1992 and 2001–2002, he trained the Austrian ski jumping team. In 1993–2001 and since 2002, he has been director of Nordic skiing in the Austrian Ski Federation (ÖSV). He is also the ski jumping expert for German TV channel ZDF.