In 1936 the team slipped back to local city league competition and after the outbreak of World War II played progressively fewer games.

In 1943–44 Prussia briefly partnered with longtime local rival Eberswalde SV 1912 (originally FC Britannia) as a combined wartime side or Kriegspielgemainschaft.

A re-organization of the league structure that year meant that the club would no longer have to regularly face strong teams from Potsdam and Lausitz in their division and they capitalized by taking district titles in 1955 and 1956.

After the merger of the football leagues of the two Germany's Eberswalde took up play in the Amateur Oberliga Nordost-Nord (III) where they spent two seasons before being relegated to the fourth division.

The club played in the Oberliga Nordost-Nord (IV) and in the last dozen years has typically earned lower table results, before being relegated to the Verbandsliga Brandenburg in 2007.