It operated camouflaged as the Institute for Research of Antiquity, lodged in the expropriated mansion of the wealthy German-Jewish family of Oppenheim.
The institute was first headed by the Georgian émigré scholar Michael Achmeteli, who was succeeded by the Austrian professor Hans Koch.
In 1942, during the increased Allied bombing raids, the Wannsee Institut was evacuated to Schloss Plankenwart near Graz, Austria.
During this period, the Wannsee Institut was closely associated with the group preparing Operation Zeppelin, aimed at recruiting Soviet POWs for espionage and sabotage behind the Russian lines.
After the war, the surviving material of the Wannsee Institut's valuable holdings was transferred to the Gehlen Organization, an intelligence agency in the United States-occupied zone of Germany.