This paper aims to explain how Muhammadiyah, as the second largest Islamic movement in Indonesia, has significantly played peace-building role for the Bangsamoro, which is the minority Islam-based ethnicity living mostly in the southern Philippines. Series of peace talks and negotiations lead to peace agreement between the Bangsamoro and the government of the Philippines. However, reconstruction agenda remains major problem in the area. Therefore, the Bangsamoro invites overseas Islamic movement to immediately rebuild. Concerning studies on non-state actors in peace building, more people argue that the actors including NGOs have hidden political, economic and ideological agenda behind humanitarian aid, while the rest believe that they are neutral. Although Muhammadiyah is an Islamic-based movement, it has not exclusively promoted to spreading the Islamic mission, but inclusively and comprehensively worked with another stakeholders and its international counterparts to build social integrity and infrastructures. This article focuses on implementing inclusive and comprehensive prescription in peace building process taking place in the Bangsamoro, which is located in the southern Philippines. Muhammadiyah recognizes that the religious identity is the underlying factor for long period of conflict. To maintain the peace, Muhammadiyah, then, cooperates with the Catholic NGO of Italy to manage peaceful behaviors among the members of government.