Indonesia’s military modernisation programme, known as the Minimum Essential Force (MEF), is frequently associated with force structure development through defence acquisitions and the revitalisation of military equipment, aimed at equipping the Indonesian National Armed Forces (TNI) with the minimum essential capabilities to address current and future security challenges. However, the MEF also entails significant organisational transformation. Despite undergoing the most extensive restructuring since 1985, scholarly attention to the organisational development of Indonesia’s military remains limited. This chapter pursues two primary objectives. First, it provides an overview of the evolution of Indonesia’s military organisational structure across multiple levels, beginning with the broader military institution and extending to the service level. Second, it examines the role of civil-military relations in driving and shaping the organisational development of the Indonesian military. The chapter contends that civil-military relations—alongside military modernisation and capability enhancement—play a crucial role in shaping TNI’s organisational trajectory. In the context of the MEF, the analysis demonstrates that the military’s corporate interests—particularly those of the Indonesian Army—are instrumental in influencing both the pace of implementation and the scope of institutional reform.