After the Kristallnacht pogroms that took place over the night of 9 November - 10 November 1938, Bernhard Lichtenberg, a canon of the cathedral chapter of St Hedwig since 1931, prayed publicly for Jews in the evening prayer following. Lichtenberg 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 burned out completely in 1943 during air raids on Berlin and was reconstructed from 1952 up to 1963.