Executive power in EU migration policy is shifting. The theory of executive federalism broadly underpinned its initial implementation design. Instead, an increasingly integrated administration is emerging. EU agencies play a key role in this transformation. I analyse patterns of joint implementation, with experts deployed by EU agencies involved in areas such as the processing of asylum claims, and return. I scrutinize the emergence of agency functions which hold steering potential. These developments create obvious tensions with the agencies’ governance structures which are largely intergovernmental, and influenced by strong regulators. I reflect on how these internal governance structures can be squared with independence. Developments also bring to sharp relief the challenges of fundamental rights oversight and accountability. I comment on how these can be ensured in an evolving administrative landscape.