Like other synagogues in the Protectorate of Bohemia and Moravia, the New Synagogue served as a warehouse for confiscated and stolen Jewish property since October 1941. Furniture and other furnishings from the apartments of the deportees were sold off by the authorities. Any religious services were forbidden.
The synagogue building was gravely damaged during an American air raid on 20 November 1944. The photograph of the women's gallery of the synagogue after the air raid comes from the collections of the Jewish Museum in Prague.
After World War II, the Ministry of Health became the owner of both the Jewish community's administrative building and the synagogue. The synagogue continued to be used in the same way as during the occupation: as a warehouse.