Indonesia in the post-New Order era saw frequent incidents of religious violence. These began with bloody sectarian conflicts in the cities of Ambon and Poso, which pitted Muslims against Christians. During the era of President Susilo Bambang Yudhoyono (2004-2014), heresy campaigns against nonmainstream faiths (Ahmadiyah and Shi'a) increased, followed by attacks mainly levelled at properties belonging to members of these minority communities. Scholars have argued that Yudhoyono and his predecessors, Abdurrahman Wahid and Megawati Soekarnoputri, should be held responsible for this frequent violence. However, while the presidents' ideological outlooks or personalities may have been contributing factors, this article will focus rather on the institutional factors that hindered their responses to the violence. At times, the presidents encouraged initiatives to promote the rights of minorities. However, these programmes faced constraints from other state institutions due to the bureaucracy and judiciary's inclination to preserve majoritarian social order and the hegemonic interpretation of the Belief in One God article in the state's foundational philosophical theory (Pancasila). These challenges were further compounded by a decline in presidential power in the post-New Order era. This article argues that, so long as these constraints exist, any Indonesian president will have difficulties overcoming violence against minority communities.