After the Kristallnacht pogroms that took place over the night of 9–10 November 1938, Bernhard Lichtenberg, a canon of the cathedral chapter of St Hedwig since 1931, prayed publicly for Jews at evening prayer. He was later jailed by the Nazis and died on the way to the concentration camp at Dachau. In 1965 Lichtenberg's remains were transferred to the crypt at St. Hedwig's.
The cathedral was severely damaged by allied bombing in an air raid on 1 March 1943 and only the shell of the building was left standing. Reconstruction started in 1952 and on the 1 November 1963 it was consecrated by the Bishop of Berlin.