This chapter examines the Bangsamoro peace process to end civil conflict on the island of Mindanao in the Philippines. With the Philippines boasting a long history of granting amnesties for human rights violations in the context of separatist and other conflicts, and the United Nations excluded from the negotiations, this appears to be a straightforward case in which an amnesty is used to address an intractable separatist conflict. Yet, as this chapter argues, the post-settlement period reveals that the fight against impunity for human rights violations in the Philippines is far from over. Rather, the Transitional Justice and Reconciliation Commission has taken a strong, but pragmatic anti-impunity stance, argued that impunity for human rights violations is not a means of achieving peace but a cause of conflict in Mindanao, and proposed measures to institutionalise the eradication of amnesties for human rights violations in the Philippines. Directly influenced by United Nations’ policies, it has sought not only to promote accountability and anti-amnesty norms but to refute the most commonly used justification for the use of amnesties in the Philippines and, indeed, region.