Ahead of the 2012–13 season, Beck announced his intention to voluntarily resign as captain and the newly signed Tim Wiese succeeded him as captain. After not being included in a squad against Frankfurt on 1 September 2012, Beck made his first team return on 23 September 2012, in a 3–1 win over Hannover 96. However, following Wiese's injury, Beck was captain for the match against Nürnberg on 28 November 2012, which they lost 4–2. In the wake of Markus Babbel's sacking, Beck criticised Babbel after disagreements. After Wiese was stripped of the captaincy, Beck was permanently given the captaincy. Beck scored his first goal of the season in a 2–2 draw against Wolfsburg on 13 April 2013. Beck made 31 appearances and scored once in the 2012–13 season in which he helped the club survive relegation.