Scholars have been debating the role of autonomy in resolving ethnic or separatist conflict. As the conflict persists despite the application of autonomy, scholars have been trying to identify factors that make autonomy perpetuates conflict. Due to ongoing humanitarian concerns in Papua, this article discusses how special autonomy (SA) has affected conflict in this region. Different from existing studies that tend to disregard comprehensive dimension of autonomy and focus merely on the role of institutions in conflict, this study examines institutionalisation of SA by scrutinising its three facets (relationship between SA institutions and their external environment, institutional changes and continuities, and internal dynamics of local institutions) in three dimensions of autonomy (political, fiscal, and administrative). This article shows that the institutionalisation of special autonomy in Papua has perpetuated separatist conflict and led to various internal conflict because it is impaired by three issues. First, external influences and pressures particularly from central state do not conform to local needs, values, and expectations. Second, institutional change and continuity are uncertain and ceremonial due to a combination between the domination of the central state and unresolved political contestation in the local dynamics. Third, internal dynamics of institutions are marked by competing logics and forms of dissociated agency due to the ambiguity of institutional rules and structures alongside ethnic contestation.