COVID-19 presented Europe with an, in many respects, unprecedented challenge. While the virus proved itself to be transnational in nature, not taking heed of borders, government responses were largely national. Still, governments soon found themselves engaged in complex multi-level policy cooperation at the national, subnational, and supranational levels. This paper looks at the crisis response in the Low Countries (Belgium and the Netherlands) to understand the impact of this process on the political system. We argue that efficient multi-level policy cooperation in both countries has run up against the limits of existing institutions, leading to significant political grievances. In Belgium, slow negotiation between the central and regional governments has put the federal system in question. In the Netherlands, meanwhile, the absence of European institutions tasked with fiscal policy coordination has increased the salience of the EU fiscal sphere once again.