The article addresses the institutional role of the EU in the Council of Europe, with particular emphasis on EU participation in Council of Europe treaties and EU accession to the ECHR. While recognising the joint effort to achieve greater unity in the region of Europe through respect for the shared core values of pluralist democracy, human rights and the rule of law, the concerns raised by non-Member States of the EU about the impact of EU law and policies on the Council of Europe’s standards are examined. It is argued that the Council of Europe and the EU have a shared responsibility for upholding the effectiveness of their respective frameworks and ensuring that any overlapping competences do not create conflict. This is particularly evident when it comes to the European system for the protection of fundamental rights, which is characterised by overlapping standards and procedures. The existing cooperation between the Council of Europe and the EU should be strengthened through a more rational, rules-based approach. In particular, it is suggested that the two systems should jointly agree on a series of basic principles on the treaty-making process, providing for horizontal application by the introduction of specific rules on, for example, voting and speaking rights of the EU, the sharing of reporting obligations between the EU and its Member States under Council of Europe monitoring mechanisms, and financial arrangements. The EU’s participation and financial contribution to monitoring follow-up should always be considered on a case-by-case basis, taking into account the specificities of each mechanism.