Shortly after the formation of the league, the Nazis reorganised the administrative regions in Germany, and the Gau East Prussia the Prussian province.

The two top teams of each division then entered a finals round which consisted of two four-team groups.

The bottom two teams were supposed to be relegated but the increasingly restrictive politics of the Nazis meant, that the club of the Polish minority, KS Gedania Danzig, had to resign from the league and was disbanded.

In January 1940, the competition was cancelled altogether and four selected teams played a Gauliga championship tournament instead.

The Gau Ostpreußen was in itself enlarged when parts of occupied Poland were added to it from the end of 1939.

The imminent collapse of Nazi Germany in 1945 gravely affected all Gauligas and football in East Prussia ceased in 1944 due to the arrival of the Red Army in the region.

With the beginning of the East Prussian Offensive in January 1945, the region was completely engulfed by war.