Objectives. Turkey, Algeria, and Pakistan have been persistently challenged, since their founding, by both Islamist and ethnic separatist movements. These challenges claimed the lives of tens of thousands of people in each country. I investigate the causes behind the concurrence of Islamist and ethnic separatist challenges to the state in Turkey, Algeria, and Pakistan. Method. This research employs comparative historical analysis, and more specifically, a most different systems design. In addition to small-N cross-national comparison, I also designed an intertemporal comparison, whereby Turkish, Algerian, and Pakistani history is divided into four periods, corresponding to preindependence, mobilization for independence, postindependence secular nation-building, and Islamist and ethnic separatist challenge periods. Results. Contrary to the prevailing view in the scholarship, this article formulates an alternative reinterpretation of Turkish, Algerian, and Pakistani nation-state formation. These three states were founded on the basis of an Islamic mobilization against non-Muslim opponents, but having successfully defeated these non-Muslim opponents, their political elites chose a secular and monolingual nation-state model, which they thought would maximize their national security and improve the socioeconomic status of their Muslim constituencies. The choice of a secular and monolingual nation-state model led to recurrent challenges of increasing magnitude to the state in the form of Islamist and ethnic separatist movements. The causal mechanism outlined in this article resembles what has been metaphorically described as a “meteorite” (Pierson, 2004), where the cause is short term (secular nationalist turn after independence) but the outcome unfolds over the long term (Islamist and ethnic separatist challenges). Conclusion. A distinct and counterintuitive path of nation-state formation has been identified based on the cases of Turkey, Algeria, and Pakistan. This research demonstrates that a contradiction between the goals of the original mobilization that establishes the state and policies of its postindependence governments can be a major structural source of instability and violence in the long run. These findings suggest that theories of nationalism that were developed based on the European experience of ethnic or linguistic nationalism need to be modified in explaining the religious nationalism that is found in the origins of some of the major nation-states in the Muslim world.