This article examines the development of a cap on the use of so-called ‘project credits’ in the EU emissions trading scheme. It investigates how the issue of such a limit was addressed in the negotiations of the Linking Directive, and how it has been dealt with in the later implementation of this directive. The article applies two explanatory approaches: one based on intergovernmentalist theory, assuming that the cap reflected the preferences of the EU Member States; and one based on the multi-level governance model, assuming that the cap expressed the preferences of EU institutions rather than Member States. What is found is a two-stage development: during the negotiations of the Linking Directive, Member States managed to secure a no-cap solution allowing extensive use of the project credits. In the later implementation phase, however, when the emissions trading scheme was up and running and a certain legitimacy for the system had been established, the Commission managed to ‘regain control’ by bringing back a cap. Thus, the project credit cap—and by that, the very nature of the EU emissions trading scheme—has been the subject of a continuing power struggle within the EU—and different theoretical perspectives explain different stages of this process.