In the expansive realm of research and innovation (R&I), the European Union (EU) is recognized as a model of ethical governance. However, this admirable position coincides with a compelling quest for legitimacy within the EU's institutional framework, presenting a paradox. This situation highlights a two-tier governance system: one that is paradigmatic and another that lacks ethical legitimacy. Furthermore, the EU’s ethics system is multifaceted and marked by fragmentation, which arises from diverse interpretations of ethics, ranging from normative ethics to superficial legitimation processes. This division between ethics and legitimacy exacerbates the fragmentation. This chapter explores this paradox across different ethics systems. While prevailing literature often examines the interplay between input, output, and throughput legitimacy, I argue that these distinctions are evolving. Participatory mechanisms, once central to input legitimacy, are now shifting towards a performance-oriented approach. Additionally, the EU’s ethics system is fragmented in two main respects: (i) the relationship between ethics and legitimacy and (ii) the sources of legitimacy, which may include normative ethics or public participation mechanisms. This fragmentation not only leads to potential ethical disconnects but also challenges the existence of a unified ‘ethics system’. This chapter aims to dissect the complex relationships between R&I governance and broader institutional ethical considerations, prompting a critical reassessment of EU governance from an ethics standpoint.