The club's greatest success came in 2012 when it qualified for the new southern division of the expanded Bayernliga, the fifth tier of the German football league system.

After two more seasons where the side narrowly escaped relegation Affing improved, culminating in a league championship in 2002–03 and promotion to the Bezirksoberliga Schwaben.

[1] FC Affing quickly adapted to the new league, coming fourth in its first year there and second the following season, thereby earning promotion to the Landesliga Bayern-Süd.

Changes to the league system in Bavaria at the end of the 2011–12 season meant the unique opportunity for the Bezirksoberliga champions to earn promotion to the Bayernliga and Affing was successful at that, overcoming TSV Landsberg and FC Gundelfingen in the process.

[5] In October 2013 the club announced that it had to cut the salary of its players by up to 70 percent because of financial difficulties caused by an outstanding tax dept.