The current EU approach to jurisdictional conflicts is discussed in the first part of this article. The article highlights the persistent problems of the existing legal framework as well as those emanating from Eurojust’s approach to the matter. After linking the topic with the ne bis in idem principle, the Member States’ interests in prosecuting criminal offenses under their competence, and the EU’s objective in the AFSJ when fighting impunity, the author presents some pivotal reflections on a better solution in the second part. Any solution first and foremost has to respect the EU’s main characteristic as a supranational organisation aligned to its constitutional treaties and to its Charter of Fundamental Rights. Within this framework, the article: Opts for models that not only solve but also prevent conflicts of jurisdiction; Highlights the possibility of distinguishing between more flexible and less flexible models; Illustrates a model based on the territoriality principle (locus delicti criterion) for both the assignment of jurisdiction and conflict resolution; Advocates a model with definitive and binding jurisdictional rules on: forum selection, proceedings and rights of concerned persons, arguing that it is of secondary importance whether such a model would be construed horizontally (i.e., through interaction between competent state authorities) or vertically (i.e., by giving a substantial role to Eurojust and the ECJ). The article also discusses other critical issues that are affected by the EU’s choice to safeguard the ne bis in idem principle within the framework of preventing and solving jurisdictional conflicts, e.g., the exclusion of parallel investigations, the rights of suspects and victims to intervene in the proceedings judicial review of the relevant decisions, etc. Lastly, it addresses the legal basis of the EU’s competence to regulate jurisdictional conflicts and the proper legal instruments to be used according to the characteristics of the model chosen.