On September 16, 1939, the church was closed by German army and the missionary aisle taken over to be used as a warehouse by German troops and police. The building was desecrated, its equipment stolen. During their withdrawal from the city, retreating German forces set fire to the edifice on January 19, 1945, which lasted three days. The incoming Soviet troops fired artillery shells at the church, severely damaging the dome and causing another fire on the residential part of the attic.