This paper analyses how the Court of Justice of the European Union resolves conflicting situations surrounding intellectual property rights (IPR). More specifically, it looks into how it approaches clashes of IPR with other fundamental rights and economic freedoms and with what consequences. Building upon previous literature, I advance the argument that the resolution of the conflict, by means of the proportionality interest-balancing exercise, pursues a pro-harmonisation agenda not only in the obvious context of free movement, but also in the setting of fundamental rights. I show that the recent Coty Germany ruling is likely to accelerate this trend because of its recognition of positive obligations of the Member States in the context of fundamental rights. It is argued that this could also be used by national courts to improve an existing IPR framework, in particular by filing preliminary references that question legislators’ choices such as non-implementation of permissible exceptions and limitations. After highlighting the importance of maintaining a separation between different policy levels (secondary law vs Charter), I outline why Coty Germany is a very worrying reading of Article 17(2) of the EU Charter, and suggest that this could be remedied by synchronising its interpretation with the Court’s doctrine of ‘specific subject matter’ in the context of free movement.