The Lisbon treaty left the European Union (EU) common security and defence policy (CSDP) as an intergovernmental instrument. Formally, decision-making is subject to unanimity amongst the member states. Recently, however, studies have challenged the assumption that policy-making within the main lies with elected member states’ governments. Instead, studies suggest that although its formal delegated powers are limited, the Commission de facto informs policy decisions within CSDP. Commission influence in the CSDP has however not been studied systematically. Aiming to fill this gap in the literature, this paper asks if and if so how the Commission’s de facto influence differs from its formal role within the CSDP. Two cases where one would not expect the Commission to influence policy-making are analysed. (1); the launch of EU military missions and (2); the development of an EU Maritime Security Strategy. The analysis shows that the Commission is de facto strongly involved in EU security and defence policy-making and that it also has influence over the decision-making outcomes. This influence is linked to the EU’s increased focus on having a comprehensive approach to security and defence issues and in particular the Commission’s ability to exploit its financial powers and right to initiate within interlinked policy areas such as external development and internal security. However, the Commission also influences CSDP decision-making by forming alliances with member states who share its interests and by providing technical and legal expertise.