This article aims to contribute both theoretically and empirically to the study of political parties in the EU context, focusing on party organisation. Theoretically, it draws on insights from various literatures to develop a novel typology of multilevel party organisation specific to the EU context. It argues that parties are goal-seeking actors that choose their organisation based on a cost-benefit analysis, involving both party characteristics and the institutional context. Empirically, the article applies this framework on the Flemish political parties. It finds that rational goal-seeking behaviour cannot fully account for parties’ organisational choices. Results show that normative and historical considerations play a crucial role in parties’ cost-benefit analysis. It therefore calls upon future research to expand the number of comparative studies and to further assess parties’ goal-seeking behaviour regarding their multilevel organisation.