In the 2006–07 season, Compper made four appearances for the reserve team in August 2006. On 14 October 2006, he made his first appearance (as well as his first start), in a 3–1 win over Wolfsburg. Because of the injuries of both Filip Daems and the national defender Marcell Jansen, he became a regular player in the autumn of 2006 in the Bundesliga. He had a handful of first team appearances until he was dropped from the first team after criticising Manager Jupp Heynckes following a 1–1 draw against 1. FSV Mainz 05 on 9 December 2006. On 30 January 2007, he returned to the first team from suspension, in a 0–0 draw against 1. FC Nürnberg, in what turned out to be Heynckes' last game as Manager. Following Heynckes' resignation, Compper was given more first team opportunities under new manager Jos Luhukay. He finished the season with 23 league appearances, but the club was relegated at the end of the season, finishing last in the Bundesliga table.