In the context of Russia's war against Ukraine, the Baltic states have witnessed an escalation in tensions surrounding their local Orthodox churches affiliated with the Moscow Patriarchate. This dynamic is compounded by the long-standing practice of the Russian Orthodox Church leveraging its international infrastructure to advance Russian foreign interests. Consequently, parishes under its jurisdiction have come under scrutiny, accused of disseminating Russian war propaganda and imperial claims within European nations. The governments of Estonia, Latvia, and Lithuania have adopted varied approaches in their management of the local Orthodox churches belonging to the Moscow Patriarchate, which represent a minority in all three countries. These approaches are further influenced by the activities of the churches themselves and the reaction of other religious communities to the political measures taken against them. The present paper contextualizes these variations within the broader framework of the securitization of religion and European conceptualizations of religious freedom. The study seeks also to address the question of how a balance between security and religious freedom can be achieved in the context of hybrid warfare.