The political relationship between Islam and the state in Indonesia has been largely a story of mutual antagonism and distrust. This adversarial relationship has been due primarily, but not wholly, to the conflicting ideas among the nation's founding fathers, the majority of whom were Muslims, on what constituted an ideal Indonesian independent state. Crucial in the debate was whether the state should be “Islamic” or “nationalist” in character. The former necessitated that Islam, given its holistic nature and the fact that it is professed by the majority, be adopted as the ideological basis of the state. On the ground that Indonesia is socioreligiously heterogeneous, for the sake of the country's unity, the latter required that the state be based on a “deconfessionalized” ideology — Pancasila.

The fact that such ideological discourse instigated conflict was not so much because of the different degree of religious devotion among the Muslims — a notion which underpins the famous santri–abangan and Islamic–secular (or religiously neutral) nationalist concepts. Rather, it was due largely to the inability of the nation's political elite to negotiate and reconcile those differences, as if Islam and nationalism are mutually exclusive entities.