The ratification of the Prespa Agreement between Greece and North Macedonia marked the end of one of the longest diplomatic disputes in Europe. EU officials were quick to praise the agreement not only as a positive example for resolving bilateral disputes in the Western Balkans, but also as an illustration of the power of attraction of the EU. Nevertheless, while it is undeniable that the agreement aligns with EU strategic interests and its normative agenda of transformation of its near abroad, we argue that a closer look into the history of the dispute and the ratification process in each country reveals tensions that cut across the internal governance of the EU and the conduct of its external relations. Our analysis of the Prespa Agreement as an instance of this internal-external nexus of EU governance showcases lingering stresses that today’s mode of European integration generates between state elites, EU institutions and democratic communities across the EU’s internal and external periphery.