Political parties in EU member states are situated in a complex multilevel polity, having to engage with their domestic political reality together with EU politics and international linkages with fellow European parties. But how do these parties organize? This research intends to understand how competing, though not mutually exclusive logics of political behaviour can help explain the variations in how parties apprehend this multilevel context. Relying on a rich empirical strategy with 68 semi-structured interviews with European and national party elites in 19 national political parties from Belgium, Denmark and the Netherlands, supplemented by a party statutes investigation and data gathering in the Chapel Hill Expert Survey, we conduct a Qualitative Comparative Analysis (QCA). It starts from the broad assumption that parties’ multilevel organization needs to be contextually understood, relying on both past and current party dynamics, as well as the actions of the (senior) individuals populating party organizations. Our analysis shows that parties’ different multilevel organization is the result of an interaction between various factors, crucially party genetics and individual agency.