Contemporary conflicts of sovereignty in Europe have gone beyond the clash between national and supranational sovereignty. Sovereignty conflicts are increasingly occurring within member states. This paper develops a conceptual framework that distinguishes between foundational, institutional and territorial conflicts of sovereignty, elaborating on this taxonomy with reference to the historical evolution of the concept of sovereignty in Europe. It provides an account of why we have seen a proliferation in conflicts of sovereignty within European states. This is due in part to the notion of “shared” sovereignty. Central to European integration, this notion has introduced considerable institutional indeterminacy into the political systems of member states, leading to many of the institutional conflicts of sovereignty we see in Europe today. The struggle of national party systems to institutionalize societal conflict via partisan competition is another contributory factor. This has displaced conflict onto the terrain of how popular rule is institutionalized within the national state. In developing this framework, the paper provides a method for distinguishing between political conflicts tout court and those touching specifically upon sovereignty. Moreover, the framework helps us distinguish between those conflicts of sovereignty most destabilizing for a polity and those which are less so.