The growth of European Union (EU) competences in the field of external security in the last decade has produced a substantial increase in the number of EU institutions and bureaucratic actors engaged in the planning and management of these policies. Moreover, the expansion of competences in such a sovereign sensitive area comes up against the persistent intergovernmental nature of the security sector. This has resulted, on the one hand, in a complex institutional architecture with heavy demands in terms of coordination, and on the other hand, in a stark differentiation and stratification of the legal regimes with a potential to impact on policy outcomes. This state of uncertainty is particularly relevant when looking at relations with countries bordering the Union, as the long-standing web of interactions there has developed a more complex institutional environment. While most of the scholarly literature focuses on single institutional sectors or policies (Common Security and Defence Policy, European Neighbourhood Policy, or the external side of the Area of Freedom, Security and Justice), this study seeks to address the issue with a comprehensive analysis of the institutional framework that has emerged in the last decade, more notably, since the entry into force of the Treaty of Lisbon. The article provides, first, an overview of the EU's institutional actors responsible for security policies in the regions bordering the EU, and second, an examination of the different mechanisms established to address the coordination issue. Finally, this study will argue that the traditional military dimension is but one, and certainly not the most developed, of the security instruments employed by the EU. At another level, it will be argued that the shift of focus from the military to other security tools has altered the institutional balance in the security sector, substantially adding to the relative influential weight of the Commission.