​In recent years, the Estonian government has expressed concerns regarding the former Estonian Orthodox Church of the Moscow Patriarchate (MPEÕK) due to its affiliations with the Russian Orthodox Church, especially in light of geopolitical tensions following Russia's invasion of Ukraine in 2022. The Estonian Ministry of the Interior has advocated for the MPEÕK to sever canonical and legal ties with the Moscow Patriarchate to safeguard Estonia's national security interests. ​

In January 2024, the situation escalated when Estonia declined to renew the residence permit of MPEÕK's leader, Metropolitan Eugene (Valeri Reshetnikov), citing his consistent support for the Kremlin's actions in Ukraine as a security risk. Metropolitan Eugene departed Estonia in February 2024.

The MPEÕK made amendments to its statutes in August 2024, removing explicit references to the Moscow Patriarchate and asserting administrative, economic and educational independence. However, the Ministry of the Interior deemed these changes insufficient, viewing them as largely symbolic and asserting that the Moscow Patriarchate's influence remained intact.

​In March, the Estonian Supreme Court declined to process appeals submitted by the Estonian Orthodox Church of the Moscow Patriarchate (MPEÕK) and the Pühtitsa Convent regarding the Estonian parliament's declaration labeling the Russian Orthodox Church as supportive of Russia's military aggression.

The appellants argued that the parliament exceeded its authority and violated their right to be heard by not consulting them before making the declaration. They also contended that the declaration unjustly implicated MPEÕK and the Pühtitsa Convent, which operate independently under Estonian law, potentially fostering hostile attitudes towards them.

Complicating matters further, the MPEÕK sought to rename itself as the Estonian Orthodox Church. This proposal faced opposition from both the Estonian government and the Estonian Apostolic Orthodox Church (EAÕK), which is under the jurisdiction of the Ecumenical Patriarchate of Constantinople. Critics argued that the proposed name was misleadingly similar to the EAÕK's official designation and could imply representation of all Orthodox Christians in Estonia, which was not the case.

The MPEÕK Synod decided to change the church's name to the Estonian Christian Orthodox Church at its sitting on January 10, 2025. Legal challenges to the name change were overcome in March of 2025 when the Tartu County Court ruled that the church's new name is not at odds with its activities, their scope, extent or legal form.

According to planned amendments to the Churches and Congregations Act, a church, monastery or congregation operating in Estonia must not be directed or, through its bylaws or finances, connected to a governing body, spiritual center, religious leader or organization based abroad that poses a threat to Estonia's national security, public or constitutional order. Such connections are also prohibited with individuals or institutions that promote war, commit acts of terrorism, incite violence or support military aggression.

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