The EU's response to the European 'refugee crisis' has involved parallel efforts to strengthen the EU's capacity for external migration management in the domains of CSDP and AFSJ. To provide a swift response to the 'refugee crisis' in 2015, EU member states decided to utilise existing operational CSDP capabilities as a short-term foreign policy tool. Simultaneously, we have seen an impressive strengthening of the mandate and capabilities of ASFJ actors in external migration governance. Although institutional links between civilian CSDP and AFSJ have existed for over two decades, the parallel task expansion has created new demands for inter-institutional coordination between the two policy areas. Combining neofunctionalist theory with insights from research on inter-institutional overlap, this article argues that responses to neofunctionalist spillover pressures may trigger inter-institutional dynamics, which can involve both cooperation as well as conflict. Empirically, we find that these inter-institutional interactions have had important implications for integration in both policy areas, which cannot be fully understood by studying these policy domains in isolation.