In the 2012–13 season, Compper continued to feature in the first team as a centre–back position after an appointment of Markus Babbel. In absence of Tim Wiese, Compper was given the captaincy role in September 2012. The club won back to back matches against Hannover 96 and Stuttgart. He started in every match until his sending off for a second bookable offence, in a 1–1 draw against Fortuna Düsseldorf on 10 November 2012. Compper also captained the side four more times until he was dropped from the first team in January 2013 over a comment he made about the club. As a result, he was demoted to the U23 side. In addition to being dropped, Compper was in a contract negotiations. By the time of his departure, Compper made 16 appearances in the 2012–13 season.