The contemporary challenges and crises in South Sudan cannot be fully explained without attention to the historical entanglement between the Christian Churches, ethnic identities, and socio-political stratifications. While much attention has been given to the positive contribution of Christian Churches under the auspices of the South Sudan Council of Churches to maintaining peace and harmony in the country, less attention has been given to their roles in sustaining the social divisions. With a special focus on the three major Christian Churches in South Sudan (Catholic, Episcopal (Anglican), and Presbyterian), this paper analyses how the peculiar identities of these Churches sustain social divisions among the people, thereby hampering ongoing reconciliation in the conflicted country. To achieve this, I will first highlight how colonial structures shaped these churches over time and how they intersect with various contemporary ethnic divisions in the country. I will then analyse the Action for Peace, a major reconciliation initiative of the South Sudan Council of Christian Churches, and its implementation by the named churches. This will be followed by delineating the limitations of this process, as a result of distinct Christian identities in the country. Finally, I will highlight how the theological decolonial approaches to reconciliation can offer a pathway to sustainable peace in South Sudan.