The African Union's (AU's) doctrine underlying Peace Support Operations (PSOs) highlights the fact that the AU should take the lead in providing political direction for all AU PSOs. This includes mainstreaming the standards and operating procedures applicable to the Protection of Civilians (PoC). The PoC guidelines mandate the AU to support and complement the efforts of the host state by enhancing its capacity to secure civilians and prevent abuse against them. The guidelines have allowed the AU to develop and grow its institutional capacity and emerge as the continent's leading institution. It provides fragile member states with technical support through African-led and AU-mandated missions (crafting the concept of operations, training and implementation and procedures for peace operations). However, little is known about how the AU transfers its PoC policy to member states during peacekeeping missions. This paper assesses the institutional capacity of the AU and its ability to influence specific national PoC policies and approaches through AU PSO and United Nations Peacekeeping Operations (UN PKOs). The paper highlights that although the AU has made progress in PoC policy, it has not been implemented effectively and practically in South Sudan and Somalia, despite being a significant priority for the organisation.