Schaaf began his coaching career during his active career. He was then coach of Werder's youth teams U17 (1987/88) and U19 (1988 - 1995). 1993 till 1995 he was assistance coach in the first team. After four years as coach with the second team he became coach of the first team in 1999. He is still coach. He is the longest serving coach in today's German Bundesliga. As coach of the first team he won the German Bundesliga in 2004 and was three times Cup winner (1999, 2004, 2009). From 2004 his team qualified 5 times for the UEFA Champions League.