After World War II the club was re-established as SKG Alzenau before again taking on its pre-war name in 1947.

Like the nearby club Viktoria Aschaffenburg, FC Bayern Alzenau is a Bavarian side playing in the state league of Hesse against closer, neighbouring cities.

The club slipped as low as the Bezirksliga Gelnhausen (VII) in 1998 before working its way back up.

In 2008–09, FC Bayern Alzenau achieved promotion to the Regionalliga Süd despite coming second behind SC Waldgirmes, as only two clubs applied for a Regionalliga license, Alzenau and Rot-Weiss Frankfurt.

[1] Alzenau was unable to survive at this level however, coming last in the Regionalliga and being relegated immediately, back to the Hessenliga.