In this article we seek to address the emerging role of the European Union (EU) as a security and intelligence actor from the perspective of counter-terrorism. Intelligence as a process and product has been strongly promoted by the EU as a useful and necessary tool in the fight against terrorism, radicalization, organized crime and public order problems. A range of agencies has been established that collect, analyze and operationalize intelligence in view of strategically defined security threats. Examples are Europol and Frontex. This article makes an inventory of their roles and competences in the field of intelligence and looks at the list of instruments that encourage the sharing of intelligence between different law enforcement and security agencies. Moreover, it is argued in this article that as intelligence becomes more hybrid and as the EU only holds light powers of oversight on ownership and integrity of data, considerable governance challenges lurk around the corner. As ‘intelligence’ is usually a complex and sensitive product, it often travels outside formal bureaucratic channels, which undermines accountability and transparency of where, how and for what purpose the intelligence was gathered.