The horrific violations committed in South Sudan’s civil war led to the establishment of mechanisms ensuring the prosecution of serious crimes and reconciliation within communities shattered by war. Through a peace deal, three mutually supportive but independent institutions of transitional justice were formed: The Commission for Truth, Reconciliation and Healing, The Hybrid Court for South Sudan and The Compensation and Reparation Authority. This article examines the extent to which these mechanisms can achieve their respective aims, and argues that prosecutions need to be implemented in an integrated manner alongside reconciliation and healing because of the massive scale of abuses and enormous number of perpetrators. The article further contends that their collaboration with local, indigenous justice mechanisms is crucial because of the latter’s extensive experience in facilitating accountability and reconciliation within divided communities in South Sudan. The article concludes that whilst a limited amnesty is inevitable, a blanket amnesty is counterproductive to the aims of transitional justice in post-conflict South Sudan. Further, the article cautions against the use of immunity, arguing that this would deny justice to victims and could lead to a rise in revenge or private retribution, lawlessness and impunity.