The multidimensionality of peacekeeping missions implies the involvement of many levels of actors fulfilling distinct functions and thus sharing responsibilities, risks and costs. This paper analyses the experiences of South African troops in Burundi and Burundian troops within AMISOM to understand the constraints and opportunities of inter-agency cooperation in the case of AU-led peacekeeping operations. Both examples show the importance of multilateralism in peacekeeping missions. The diversity of actors’ experiences and capabilities, their cooperation, and the complementarity of their specific contributions are vital when dealing with the very complex and tangled challenges facing a conflict country. Several factors, including financial and military capacities, actors’ own interests, domestic politics, policies, and standards, influence the level of trust and the nature of cooperation between actors and their positioning.