From the 1990s until today, the dominant framework for understanding EU migration and asylum politics has been intergovernmentalist, assuming that the EU serves as a venue to which member states with restrictive policy preferences can ‘escape’ to circumvent domestic constraints. However, this theoretical perspective has lost much of its explanatory power after the shift of power from member state governments to EU institutions brought about by the communitarisation of EU asylum and migration policies since the Treaty of Amsterdam (1997) and the introduction of Community law and policies since the early 2000s. Studies on EU migration, however, do not agree on the impact that EU institutions now have on policy outcomes. While some argue that the Court, the Commission, and the European Parliament are able to impose ‘liberal constraints’ on member states, other studies consider them unable to shift the ‘policy core’ of EU migration policies. Many of these disagreements stem from unspecified theoretical assumptions and very different methods to compare influence and change. Therefore, what we need today in EU migration studies is a broader set of theoretical perspectives, drawing mainly from new institutionalism and multilevel governance, to explore empirically first, the preference formation of different EU institutions such as the Commission, the EP and the Court in the field of migration; second, the interaction between EU institutions and their relative impact on policy development; and third, the impact of EU policies on the domestic politics and policies of member states. In this paper, we aim to develop a research agenda that reviews the latest developments in the field and considers the main methodological and theoretical challenges of studying EU migration policies.