The purpose of this study is not only to explain a historical approach to the formation process of the Bangsamoro Autonomous Region for Muslim Mindanao (BARMM) established in the southern Philippines but also to discuss the challenges of BARMM. The process of formation of BARMM coincides with the history of the Muslim independence movement and securing autonomy in Mindanao. Therefore, this study first describes the background and contents of the peace agreements, which were done to seek the Muslims’ autonomy between the central government of the Philippines and the Muslim rebels. The main agreements covered in this study are the Tripoli Agreement, the Final Peace Agreement, and the Comprehensive Peace Agreement for Bangsamoro. The three peace agreements aimed to secure regional security by stabilizing regional politics and disarming rebels. The solution was for The Muslims to guarantee and expand autonomy in the Muslim Mindanao region. In particular, the formation of the Autonomous Region for Muslim Mindanao as the result of the agreements can be evaluated as significant progress towards the political and economic rights and self-determination of Muslims. However, despite such positive evaluation, the implementation of a nascent autonomous region (e.g., Autonomous Region for Muslim Mindanao) failed as a social experiment due to the incompleteness of the peace agreement, the government’s lack of capacity to implement the agreement, the power infighting between Islamic rebel groups, and the inequality among Muslim ethnic groups. Learning from the previous failure, the most recent Comprehensive agreement for the Bangsamoro introduced a new political body with more substantial autonomy. The new creature included the parliamentary system and a broader sense of autonomy in the administrative, legislative, and judicial systems. Although it implies practical political changes in Mindanao because the central government has made institutional arrangements to form the local authorities, such as the Bangsamoro Transition Authority and the Interim government, for power succession, it is also true that there are doubts as to whether it will succeed despite this political upheaval. So, this study additionally explains the challenges that BARMM faces and the implications that must be solved for the new Muslim autonomous government to succeed.