The original shape of the church was hugely innovative, particularly in its size. Mosaics, inside the church commemorate the life and work of Kaiser Wilhelm I. However, during World War II, Allied bombers destroyed the church in a raid on Berlin in 1943. The only part of the original building, which remained were the ruins of the belfry, more commonly known by the locals as der Hohle Zahn or literally 'the hollow tooth'. Local people chose to keep the remains in memory of the ravages of war.

Between 1951 and 1961, the new Kaiser Wilhelm Gedaechtniskirche was reconstructed next to the site of the old one; the project was overseen by Egon Eiermann. The new church features a cross, made from the nails from the old Coventry Cathedral, which was similarly destroyed by German Luftwaffe attacks during the World War II. The reconstructed church was opened on May 25, 1962, the same day as the new Coventry Cathedral. Besides the Coventry Cross the new church is home to a Russian Orthodox Iconic Cross, with a representation of the 'Stalingrad Madonna', which was designed by Lieutenant Kurt Reuber in December 1942 in Stalingrad. The Iconic Cross was placed at the front wall of the church in remembrance of hundreds of thousands of soldiers from both opposing sides who suffered and died during the war; it represents a message of reconciliation between the countries involved in the fighting.

In December of 2007, Charles Jeffrey Gray, a former British pilot who was involved in some of the World War II bombing raids over Germany, joined the campaign to help rescue the Kaiser Wilhelm Memorial Church from decay. After he learned about the condition of the church, Gray contacted Wolfgang Kuhla, the Chairman of the church's board of advice and suggested that the tower should be restored. In response, a fund was started to help raise money needed for the major reconstruction. Before the bombings, the tower was 113 metres high, but it was reduced to 68 metres afterwards.

The new church has the capacity to hold over 1,000 people. Its impressive floor is covered with unglazed ceramic tiles, of different colours and sizes. The statute of Jesus Christ was donated by the Bishop of Otto Dibelius, on the 20th anniversary of the revolt in 1944. Inside the building there is also a memorial hall dedicated to Kaiser Wilhelm, who is depicted in the mosaics. The wall now represents a war memorial, for the victims of Germany and displays illustrations of the war and its after effects. Tours of the church are organised three times a day and each lasts around one hour. During the week, there are also lectures in history held at midday. Topics covered include the history of the new church and the old ruined church. Short services are held every day for one hour and on Sundays a longer service takes place.