ENThis paper is dedicated to a brief but crucially important period for Lutheran Churches in the Baltic states during the 20th century that set into motion religious processes for almost half a century. During World War II, the Baltic states – Estonia, Latvia and Lithuania were occupied by the Soviet army, later taken over by Nazi Germany and then again reoccupied by the Soviets in 1944/45. During this period and shortly after the war, Lutheran Churches in the Baltic states experienced a whirlwind of totalitarian power, different state policies towards religion, significant loss of the clergy and church members, and faced the demolition of churches as institutions and places of worship. In these times of changes, the members of Lutheran leadership of Estonia and Latvia in 1944 were forced to leave their states and churches, never to return, as the Iron Curtain descended between the Soviet Union and the Western world after the war ended. A similar situation occurred with Lithuanian Lutherans. The author seeks to explore the changes in Baltic Lutheran Churches and their leadership from 1944–1949 by analysing the situation in each church separately and seeking similarities in the process of leaving the church in the hands of other church members, – those, who stayed behind in the occupied territories.Through persons and their attitude towards the new role as the church leader(s), the author investigates the sovietisation process of the Lutheran Church (and overall – the religion) that was aggressively carried out by the Soviet state in the Baltics in the last months of war and the first post-war years until the mass deportations in March of 1949, which frame the chronological period of the paper. Sources from the archives in Estonia, Latvia and Lithuania are used to describe and illustrate this process, the existing research on the changes of leadership of the churches has largely omitted all three Baltic states due to the language barrier or academic research tendencies.