The legal framework governing the functioning of the European Public Prosecutor’s Office (EPPO) is founded on the integration of Regulation (EU) 2017/1939 (the so-called EPPO Regulation) with the domestic legal systems of EU Member States. The EPPO Regulation is far from self-sufficient and, in several respects, explicitly refers to national law. This hybrid architecture gives rise to previously uncharted challenges in the field of judicial cooperation in criminal matters within the EU, especially considering that the establishment of a European prosecutor has long been viewed as a step towards vertical integration in criminal justice – a goal that remains only partially achieved. This contribution examines some critical issues arising from the EPPO legal framework. Specifically, it first considers the criminalisation of offences falling within the EPPO’s material competence (the so-called PIF offences), to assess compliance with the obligations imposed by the PIF Directive. It then addresses the mechanisms of domestic scrutiny – judicial in a broad sense – over the EPPO’s exercise of competence during investigations. Finally, it analyses the functioning of transnational investigations under the Regulation.