Following the German invasion of 1941, Merzhanov was involved in defense projects in and around Moscow, and stayed in the city when the Academy of Architecture evacuated to Chimkent. In August 1942, Merzhanov, his wife and his associates were arrested. On 27 February 1944 he was extrajudicially sentenced for 10 years in labor camps for Anti-Soviet activities. According to the sentence, testimonies against Merzhanov were produced in advance in 1938, and both witnesses were executed in the same year. Merzhanov was lucky enough to be sent to Komsomolsk camps where city authorities, who collaborated with him as a free professional in the 1930s, extricated him from the barracks. For the next five years he headed a construction sharashka. Merzhanov's public building in Komsomolsk follow the Stalinist style of the late 1930s. Meanwhile, his wife perished in the camps and his son, Boris Merzhanov (1929–1983), was arrested in 1948.