In June 1940, Zhdanov was sent to Estonia to supervise the establishment of the Estonian Soviet Socialist Republic and its annexation into the USSR.
During the Great Patriotic War, Zhdanov was in charge of the defense of Leningrad. After the cease-fire agreement between Finland and the Soviet Union was signed in Moscow on 4 September 1944, Zhdanov headed the Allied Control Commission in Finland until the Paris peace treaty of 1947.
In 1946, Zhdanov was put in charge of the Soviet Union cultural policy by Joseph Stalin. His first action (in December 1946) was to censor Russian writers such as Anna Akhmatova and Mikhail Zoshchenko (Zhdanov Doctrine).
In 1947, he organized the Cominform, designed to coordinate the communist parties of Europe. In February 1948, he initiated purges in the musical area, widely known as a struggle against formalism. Dmitri Shostakovich, Sergei Prokofiev, Aram Khachaturian and many other composers fell victims to these purges.
He died in 1948 in Moscow of heart failure; Nikita Khrushchev recalled in Khrushchev Remembers that Zhdanov could not control his drinking, and that in his "last days", Stalin would shout at him to stop drinking and insist that he drink only fruit juice. Montefiore and others allege that Stalin himself was responsible for Zhdanov's death, citing Zhdanov's inability to orchestrate a Communist takeover in Finland as cause. Stalin had talked of Zhdanov being his successor but Zhdanov's ill health gave his rivals, Beria and Malenkov, an opportunity to undermine him.
His son, Yuri (1919-2006), married Stalin's daughter, Svetlana Alliluyeva, in 1949. The marriage was brief and ended in divorce in 1950. They had one daughter, Ekaterina.
He was one of the main accused people during the US House of Representatives' Kersten Committee investigation in 1953.
In the 1950s, following Zhdanov's death, there was a creative explosion in Soviet art—abstract and formal work.