Every survey that asks Europeans whether religion is important in their lives puts Estonia at or near the bottom, and the explanation is historical rather than philosophical. Christianity did not arrive in Estonia through preaching. It arrived in the thirteenth century with the Livonian Brothers of the Sword and the Danish crown, as the northern edge of a crusade, and the church that followed was the church of a German speaking landowning class that ruled an Estonian speaking peasantry for six hundred years. Lutheranism inherited that arrangement intact. The pastor was a figure of the manor.
The nineteenth century added a second layer. Conversions to Orthodoxy in the 1840s were driven in part by rumours of land and by the desire to escape German landlords, which meant that the imperial church too was entered for reasons that were not principally religious. The national awakening that followed was led largely by men who saw both churches as foreign institutions.
Soviet rule then did what it did everywhere, and the result today is a country where a majority state no religious affiliation and where Lutheranism and Orthodoxy are of roughly comparable size, the latter concentrated among Russian speakers.
Orthodox jurisdiction has been the sharpest religious dispute of the independent period. Two bodies claim the same inheritance: the Estonian Apostolic Orthodox Church, which is under the Ecumenical Patriarchate of Constantinople, and a church under the Moscow Patriarchate. The argument is about continuity, property and, since 2022, about the political position of the Moscow Patriarchate itself, which the Estonian parliament and government have addressed directly.