Do crises cause greater differentiation in European integration? Theoretically, we argue that differentiation is a legal instrument that can, in specific circumstances, circumvent intergovernmental disagreement over new treaties and laws. Against this background, we expect that crises are unlikely to cause differentiation in already existing EU regimes, but are likely to cause differentiation if the EU seeks to adopt new treaties and laws in response to crises. The resulting patterns of differentiation are, moreover, likely to reflect pre-existing, policy-specific divisions between the member states. Empirically, this study offers within-case counterfactual analyses of European integration and differentiation in the Euro and Refugee crises. Drawing on data covering the entire history of European integration, we predict the counterfactual development of differentiation by extrapolating long-term, pre-crisis trajectories to the post-crisis period. We compare these extrapolations to observed post-crisis differentiation to identify the causal effect of crisis on differentiation. We examine the crisis effect at the level of treaty law, legislation, possible spill-over effects from monetary or interior and justice policies into other areas, as well as the possibility that the EU’s crises might have delayed new member states’ accession to the Eurozone and Schengen Area.