In 1935, after the re-organization of German football under the Third Reich, Dessau played in the Gauliga Mitte, one of sixteen new upper class divisions.

In 1942, the team advanced as far as the quarterfinals of the Tschammerpokal, predecessor of today's German Cup.

After World War II, most organizations in Germany, including sports associations and football clubs, were dissolved by the occupying Allied authorities.

It was as Waggonbau Dessau that the club defeated BSG Gera-Süd 1–0 to capture the East German Cup, the most significant honour in their history.

In the early 2000s, Dessau played most of their football in the fifth tier Verbandsliga Sachsen-Anhalt, interrupted by two one-season stints in the NOFV-Oberliga Süd in 2004–05 and 2006–07.