Differentiated integration (DI) and flexibility in implementation (FI) are two forms of differentiation that can be used to cope with heterogeneity among EU member states. Given the different ways in which they do so, this article asks whether DI and FI are alternatives for each other or whether they serve different functions in EU legislation. Based on a dataset that maps the occurrence of opt-outs and flexibility provisions in EU directives, the analysis shows that DI and FI tend to be used together. A qualitative analysis of directives that combine different levels of DI and FI shows that, within that overall pattern, DI is used to accommodate individual outliers, while FI is used to address widespread concerns among member states. This suggests that DI and FI are two forms of differentiation in the EU, which are used to address different aspects of a common underlying set of concerns.