This chapter explores how the framework of unevenly enacted national peace agreements (NPAs) infiltrated this “peace” into existing rebel-led local peace agreements in rebel-administered areas. It focuses on the national peace agreements (NPAs) between the Moro Islamic Liberation Front (MILF) and the Government of the Philippines. Then, based on ground data collected first-hand in rebel communities, the case study depicts two inter-community peace agreements between MILF communities and non-rebel communities that were developed well before the NPAs. Where the rebel group developed “quasi-government”, how have the rebel communities applied the governance capacity to inter-community conflict resolution during their armed struggle? Can the liberal peacebuilding framework of the unevenly enacted NPAs enhance rebel-led community peace initiatives? Why could the rebel communities face systematic difficulties in managing inter-community conflict in post-NPA periods? This study illustrates transitional dilemmas for rebel communities and a blind spot of the liberal peacebuilding framework.