Central European countries with a historically dominant Roman Catholic heritage belong to a particular cluster in respect to the governance of religion. This paper focuses on Hungary and Slovakia and addresses the effect of religious nationalism on the regimes of governance of religion in the two countries. After the fall of the Berlin Wall, there was a brief period of neutral stance towards religion, which was characterized by liberal values. With the introduction of the bilateral Concordat agreements with the Holy See, both countries started to treat traditional Christian Churches preferentially. By the 2010s legislation in both countries created restrictive entry barriers for “new” religions. This created two or multi-tiered systems for “old” and “new” religions, in which the former enjoyed closer relationship with the state. As a result, the separation of church and state has become blurred. Preferentially treated churches reappeared in the public space as providers of certain educational and social services. Preferentially treated churches and the state developed asymmetrically interdependent relationships, the state having the upper hand. Meanwhile, increasingly populist and nationalist parties instrumentalized religion by involving Christianity in their nationalistic political discourse. This helped create a normative space, in which the state is able to give further preferential treatment to certain religious groups over others. The emphasis on Christian national identity underpinned these governments’ narratives that conflates migration with security and Islam, which pushed those religious groups on the margins, which do not fit in the religious nationalist narrative of the increasingly right- and populism-leaning governing elite.