Theorists of civil-military relations have for long tried to identify the specific factors that lead to weak civilian control of the armed forces in some countries and very strong oversight regimes in others. While some authors highlight the importance of structural factors (such as the level of economic modernization), others point to the crucial role of personal agency (i.e., the quality and characteristics of leadership). Obviously, some form of interplay between structure and agency does occur, but the precise patterns of this relationship have rarely been explored. This article analyses the overall strong, yet institutionally volatile state of civilian control in post-authoritarian Indonesia, and evaluates the role of structural and agency-related factors in this outcome. It concludes that Indonesia has broken its supposed path dependence in several historical, economic and political areas, suggesting that post-1998 actions by political leaders and elite groups have played a more significant role in shaping the new civil-military relationship than commonly thought.