This paper reports the findings of a comparative analysis of differentiated integration (DI) versus flexible implementation (FI). It finds overall support for our expectation that both DI and FI address international heterogeneity among EU member states and the complications in decision-making and compliance that derive from it. In addition, differentiation typically exempts individual member states in a particular situation (such as geographical location or treaty-based opt-outs) and reflects particularly high conflict in the legislative process. By contrast, our expectation that the EU uses DI in areas of core state powers, whereas FI is the instrument of choice in less politicized, market-related policy domains, receives mixed support. Finally, we observe no significant difference in the compliance effects of DI and FI. Neither instrument is sufficient to overcome the non-compliance threat emanating from imposing uniform legislation on a heterogeneous membership. This project received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement number 822304. The content of this document represents only the views of the InDivEU consortium and is its sole responsibility. The European Commission does not accept any responsibility for use that may be made of the information it contains.