This paper seeks to shed light on the current challenges facing European integration and to do so in a manner consistent with multi-level politics. It does so by taking two theoretical steps and then applying them to the current crisis of integration. First it explores a particular understanding of hegemony that enables the supranational integration process to be conceived of as a hegemonic project. Second, it introduces the structure-agency debate, which has been largely ignored in EU studies, to understand how the EU structures associated with the hegemonic project relate to underlying social processes that essentially remain located at the domestic political level. The third step is to operationalize this framework in order to show how the current domestic politicization of the European project can be understood. In this way the paper seeks to utilize recent developments in scientific realism to shed light in an innovative way on the current problems faced by the integration project.