This article considers the ongoing development of cooperation between the European Union and the North Atlantic Treaty Organization. Although institutional relations have been evolving since the Saint-Malo Declaration in 1998, efficient and coherent cooperation is still lacking; most notably at the political level. This paper seeks to investigate how the strategic foundations of the EU and NATO have developed over time, where their agendas overlap, especially regarding the ‘comprehensive approach’, and how this has affected the extent to which the two organizations have cooperated in crisis operations. The case of EU-NATO cooperation in counter-piracy is used specifically to examine both the sub-optimal cooperation at the political-institutional level and the ad hoc and informal cooperation on the ground that circumvents these formal institutional deficiencies. Ultimately, this paper demonstrates that there are, in fact, two distinct and divergent forms of cooperation developing between these two security actors.