The emergence of military ad hoc coalitions (AHCs) in Africa as a tool for conflict management outside established institutional frameworks brings about a number of questions: are they undermining existing security structures such as the African Peace and Security Architecture (APSA) or are they contributing to further regime complexity? In order to answer these questions, the article applies the logic of functional differentiation as it is used in the literature on regime complexity and inter-organisational studies. Scope conditions are developed exploring when and how functional differentiation operates and what consequences it brings about for interacting institutions. Empirically the example of military ad hoc coalitions in the Lake Chad Basin and Sahel is at the centre of analysis. It will be argued that ad hoc coalitions are part of a functionally differentiated system response within the African Security Regime Complex and not in direct competition to the APSA.