World War II led to new changes in Zenit`s history. The club came under the management of the State Optical-Mechanic Plant (later — LOMO) during the war, while the team`s players and coaches were evacuated to Kazan. Not all of the players left for Kazan though. Some stayed in Leningrad and took part in matches held during the city’s blockade. Many of the team’s players went to fight. The brothers Evgeny and Valentin Shelagin died fighting in the war, as did Nikolay Salostin, Samuil Kozinets, and Nikolay Lepeka. Arkady Larionov, Boris Ivin, and Leonid Dorofeyev did not survive the blockade.
Zenit returned to its home city of Leningrad in the spring of 1944, after which it sensationally won the USSR Cup. Zenit beat Dynamo Moscow and Spartak Moscow on its way to the final. Zenit managed to beat the “Lieutenants` team” (TsDKA) in the final. Zenit`s goals were scored by Chuchelov and Salnikov. Zenit played almost all its games in the tournament with the exact same starting 11: Leonid Ivanov, Nikolay Kopus, Ivan Kurenkov (the captain), Alexey Pshenichny, Viktor Bodrov, Alexey Yablochkin, Alexey Larionov, Boris Levin-Kogan, Nikolay Smirnov, Boris Chuchelov, and Sergey Salnikov. The team was coached by Konstantin Lemeshev.
Unfortunately, Zenit couldn`t build on this success. Year after year the team`s results worsened, and in 1948 there was even talk of breaking up the team. In 1958, Georgy Ivanovich Zharkov, from Moscow, became the first coach from outside Leningrad to head the club. Zharkov put an emphasis on cultivating players from Leningrad`s sports schools. Although the team had many natives of Leningrad, including Stanislav Zadidonov, Anatoly Dergachev, Vadim Khrapovitsky, Lev Burchalkin, Nikolay Ryazanov, and Oleg Morozov, it could not climb higher than 4th place.