At the heart of intractable conflict lies a challenging paradox: impunity is both a cause of intractability and, operationalized through the granting of amnesties, one of the key tools employed by peacemakers in their attempts to end long-running periods of violent conflict. That is, impunity is simultaneously conceived of a driver and a solution to the problem of intractability. Focusing on one of the world's most intractable conflicts, the Bangsamoro conflict in The Philippines, this article examines the nature of the impunity/intractability paradox, assesses current attempts to overcome it in the Bangsamoro peace process, and argues that a process of ‘managed impunity' introduced by The Philippines' Transitional Justice and Reconciliation Commission provides one possible way of ending impunity for human rights crimes without jeopardizing the prospects for peace.