Abstract: How, if at all, does the Commission’s expertise inform intergovernmental decision-making within the EU? In this article, we aim to capture the relationship between the Commission’s expertise and its influence within intergovernmental policy-areas through a study of Commission influence in two least likely sectors: security and defence policies (military mission Atalanta and EU Maritime Security Strategy) and external migration (EU mobility partnerships with third countries). In these cases we observe that the Commission strongly informs policy developments even though it has only limited formal competences. To explore whether and, if so, how this influence is linked to its expertise, we develop and consider two hypotheses: The expert authority hypothesis and the expert arguments hypothesis. To identify possible additional channels of influence, we also consider the relevance of two alternative hypotheses: The strategic coalition hypothesis and the institutional circumvention hypothesis. We find that the Commission’s use of its expertise is indeed key to understanding its de facto influence within policy-areas where its formal competences remain limited. Our findings add to the existing literature by revealing how expertise matters. Specifically, our cases show that the Commission informs intergovernmental decision-making by successfully linking discussions to policy-areas where it holds expert authority. However, the Commission also informs EU policies by circumventing the formal lines of intergovernmental decision-making, and by cooperating with member states that share its preference for further integration.