This article traces the institutional evolution of the Council Secretariat that plans and supports EU civilian peace operations. During the early days of the European Security and Defence Policy in the late 1990s competing political priorities of big EU member states and a dominance of military structures put civilian administrators at a significant disadvantage. Between 2003 and 2007, however, the rising number and complexity of civilian missions generated pressure for reform, which eventually led to the creation of a civilian headquarters. The historical analysis provides the basis for assessing the EU’s current institutional capacities for civilian crisis management. While some administrative capacity deficits have been addressed, increased institutional formalization and further politically motivated reforms may increase tensions and hamper the accumulation of expertise.