The British redrew from the camp after the German invasion. The camp lay deserted until September 1943, when the first 600 prisoners arrived from Larisa. This was part of a policy by the Italians, which were responsible for prisons, aiming at disbanding penal institutions in areas that were difficult to control. The first prisoners included communists that had been imprisoned by I. Metaxas and four women. Since October 1943, the Chaidari camp was the destination of an increasing number of prisoners, arrested in military blocks or by the Gestapo. They were first taken to the S.S. headquarters in Merlin Street for interrogation and torturing. .
In the end of 1943 there were about twelve hundred prisoners. The number increased in August 1944 due to
the mass arrests by the S.S.. The camp was in operation until September 1944, when the Germans started to withdraw from Greece. It is estimated that over 21000 prisoners passed through Chaidari, including the Jews, which were mostly transferred then to German camps.