Governments are adopting digital health (DH) to capture patient data and applying advanced analytics to ‘learn’ from that data. This has rendered DH data governance approaches insufficient and led to public sector decision-makers using health data without considering the public, resulting in harm and eroding trust. Yet, public sector organizations are responsible for upholding public values. How then can governments govern DH data in line with public values? To provide insights, we propose a multi-phase, mixed-methods design embedded in a public health system to identify the public’s values implicated in DH data governance and their (mis)alignment with other stakeholders’ values. Ultimately, our research will contribute to literature and practice by explaining the complexity of appropriately governing DH data and by providing the foundations for research to create a public values-oriented approach to governing DH data.