After the re-organization of German football into sixteen premier level divisions under the Third Reich in 1933, Wacker played in the Gauliga Bayern until relegated in 1938. They returned to first division football three seasons later in 1940 but were never a serious contender for the division title.
After World War II the club re-appeared in the top-flight in the Oberliga Süd in 1947. They were immediately relegated and soon supplanted by other local sides on the rise such as Bayern Munich and 1860 München. Through the 50's and 60's Wacker played third division football except for a pair of single seasons turns in the 2nd Oberliga Süd (II) early in the 50's. After the formation of the Bundesliga, Germany's new professional league, in 1963, the team settled into the Amateurliga Bayern (III) managing just three appearances in the Regionalliga Süd (II) in 1964, 1970, and 1972 before slipping to the Landesliga Bayern-Süd (IV) in 1980. They played at amateure level until being bankrupted in 2004 through the fraudulent management of the club's finances.
In the 2007-08 season, the club struggeled against relegation in the Kreisklasse 4 Wagner, the tenth tier of the league system, finishing in tenth place out of thirteen teams.