The Soviet Union officially proclaimed the separation of church and state, the equality of religions before the law, and the relegation of religion to the private sphere. Yet in practice, this model of "separation" produced a highly regulated system in which religious minorities existed within constantly shifting boundaries of legality and illegality. Although many congregations obtained formal legal status through state registration, they operated under a complex framework of state regulations that fundamentally restricted the activities of religious organizations. The limited registration of Protestant communities, and especially the establishment of a centralized religious body in Moscow in the form of the All-Union Council of Evangelical Christians-Baptists (1944) for late Protestant denominations, provided a degree of protection and visibility, including international recognition; however, this center also functioned as a mechanism of unification and disciplining of a diverse Protestant milieu and proved vulnerable during the Khrushchev anti-religious campaign. The paper demonstrates the ambivalent significance of state registration for congregations and pastors and shows how administrative manipulation of registration could serve as a trigger of pressure for the Protestant minority. Drawing on archival sources, church documents, and believers' narratives, it analyses how Protestants navigated this framework through partial compliance and negotiation, informal networks, clandestine practices, parallel religious education, and transnational contacts, while long-standing distrust that labeled them "sectarians" or "foreign" confessions generated additional layers of tension and marginalization. By focusing on these practices, the paper asks what registration actually meant under a communist regime: a limited legal status for some communities and, simultaneously, a technology of governance.