At the end of the 2012–13 season, Karlsruher SC and Arminia Bielefeld were directly promoted to the 2013–14 2nd Bundesliga.
The two promoted teams were to be replaced by Jahn Regensburg and SV Sandhausen, who finished in the bottom two places of the 2012–13 2nd Bundesliga table and thus were to be directly relegated.
At the other end of the table, Alemannia Aachen, SV Babelsberg 03 and SV Darmstadt 98 were to be relegated to the 2013–14 Regionalliga; Aachen entered the Regionalliga West.
The three relegated teams were replaced by the three winners of the 2012–13 Regionalliga promotion playoffs.
A further place in the league was available via a two-legged play-off between third-placed 2012–13 3rd Liga team VfL Osnabrück and 16th-placed 2012–13 2.