The regular season started on 17 July 2012 and finished on 25 May 2013, followed by relegation play-off games.
The league was split into a northern and a southern division, a system last in place in the 1962–63 season, expanding from 18 clubs to 37.
The division featured fourteen new clubs with only TSV Großbardorf, FSV Erlangen-Bruck, Würzburger FV and FC Schweinfurt 05 having played in the Bayernliga in the previous season.
The third placed teams of each Bayernliga division, TSV Großbardorf and BC Aichach, played the 16th and 17th placed Regionalliga Bayern teams, FC Augsburg II and SpVgg Bayern Hof for two spots in the 2013–14 Regionalliga.
All three Bayernliga clubs were relegated while the Landesliga teams of SV Raisting and VfR Garching were promoted:[7]