Post-communist transition went hand in hand with the European integration process. Much of the literature on EU accession focuses on the rational decision to implement a set of European norms into domestic legislation pre-accession. It is often concluded that once EU membership is achieved, states succumb their rationality and act on the basis of internalised norms. The paper claims that the past literature overlooks the wider framework within which policy-makers operate before and after the accession, namely domestic sovereignty over policy-making and implementation. Tracing the policy dynamics in the area of minority rights in Estonia and Slovakia, we demonstrate that the European integration ushered greater domestic control over policy implementation on minority issues in two states exposed to a heavy dose of conditionality. As we observe, both states have consolidated their state- and nation-building policies referencing EU conditionality in the course of accession and later EU membership to assert centrality of domestic objectives for policy-making and implementation.