Im Zweiten Weltkrieg wurde der Dom durch eine Flüssigkeitsbrandbombe schwer beschädigt und verwandelte die Predigtkirche mit der Hohenzollerngruft in eine Ruine. Erst dreißig Jahre später begann der Wiederaufbau der zerstörten Kirche. Im Jahre 1983 waren die Außenarbeiten am Dom abgeschlossen. Die Innenarbeiten wurden 2002 mit der feierlichen Enthüllung des achten und letzten Kuppelmosaiks beendet.

In 1940 the blast waves of Allied bombing blew part of the windows away. On May 24, 1944, a bomb of combustible liquids entered the dome. The fire could not be extinguished at that unreachable section of the dome. So the dome burnt out, part of its construction collapsed into the prayer hall. Between 1949 and 1953 the dome was closed again by a temporary roof. On May 9, 1967 the then still undivided Evangelical Church of the Union decided a committee for the reconstruction of the Supreme Parish and Cathedral Church, then located in East Berlin. The government of the Eastern German Democratic Republic did not oppose the work of the committee due to the concomitant inflow of Deutsche Marks. In 1975 reconstruction started, simplifying the building's original design and tearing down the northern wing (the memorial hall). In 1980 the baptistery and wedding church was reopened for services. The restoration of the main prayer hall was begun in 1984. On 6 June 1993 the big prayer hall was reinaugurated in an event attended by Federal Chancellor Helmut Kohl and televised nationwide in Germany.