EELC is member of the Lutheran World Federation and belongs to the Community of Protestant Churches in Europe.

When the Soviet Union invaded Estonia in 1940, most Christian organizations were dissolved, church property was confiscated, theologians were exiled to Siberia, and religious education programs were outlawed.

Although women had studied theology at Tartu University in the 1920s and some had sought ordination as priests, it was not until 1967 that the first woman, Laine Villenthal, was ordained.

[3] The Church of Estonia is episcopal in polity and is led by five bishops, including the archbishop who serves as the Primate.

"[9] Archbishop Viilma announced his support for civil unions and agreed to be a part of a panel working in 2021 on a proposal to pass a bill to define marriage as heterosexual and to strengthen the civil partnership registration with equal rights for same-sex couples.

[14] The Lutherans leaned toward opposing the death penalty, although they took no official stance, and the church does not have a committee "dealing with social-political questions".