There has been little research on élite preferences regarding supranational integration. Regional élites have been particularly neglected, even though they are implementers of European policies and programmes and therefore contribute to the integration process. To bridge this gap, this article explores the preferences of top regional civil servants – regio-crats – towards one of the most prominent supranational institutions, the European Commission. We put five explanations to the test. Support in favour of a stronger, more autonomous Commission can be driven by (1) pragmatic inter-institutional alliances, (2) the domestic distribution of power, (3) benefits derived from the integration process itself, (4) identity and identification elements and (5) transactionalism. We find support for three of these explanations as inter-institutional relations, perceived benefits and region-specific identity characteristics contribute to and account for regio-crat preferences. This resonates with interest- versus value-based approaches to European Union (EU) integration and contributes towards a better understanding of the dynamics at play in integrating multi-jurisdictional polities, of which the EU is an example.