In response to the SARS-CoV-2 pandemic, European Union (EU) Member States adopted technological solutions aimed at mitigating the effects of the virus, as well as enforcing newly adopted public health measures. Examples include apps for disseminating information, performing self-diagnosis, enforcing home quarantine orders and aiding contact tracing. This extensive use of technology for tracking and promoting public health raises important questions regarding EU citizens’ privacy. Thus far, the discourse in this regard has predominantly revolved around data protection, the risk of surveillance and the right to control access over one’s personal information (informational privacy). In light of the push towards a more unified approach to mitigating the current pandemic and future health crises through a European Health Union (EHU), we consider a different dimension of privacy that may be at risk when employing technology for public health, namely the right to non-interference with one’s decisions (decisional privacy). In particular, this article focuses on whether the advances in health-related persuasive technology, together with a more general movement towards “nudging” as an individual and public health tool, will require EU legislation to further protect decisional privacy by regulating “hypernudging” technologies and to guide the EHU in coordinating public health measures that utilise these technologies in a privacy-preserving way.