Malaysia and Indonesia are the two biggest Muslim-majority countries in Southeast Asia. The ways in which their respective constitutions address the majority religion (Islam), however, are very different. The Federal Constitution of Malaysia provides Islam as the ‘religion of the Federation’, while in Indonesia, a special constitutional recognition for the majority religion was explicitly rejected during the constitution-making process. Instead, the religion clause provides that the state is ‘based on the belief in the one and only God’. Malaysia institutionalized a federal arrangement in matters implicating Islam – individual states in the Federation retain a measure of autonomy in legislating, regulating and administering Islamic law. On the contrary, religious affairs in Indonesia remain under the jurisdiction of the national government. This paper interrogates the relationship between constitutional design, religious pluralism and its impact on religious freedom.