Background: Area-based programmes are seen as a promising strategy for tackling health inequalities. In these programmes, local authorities and other local actors collaborate to employ health promoting interventions and policies. Little is known about the underlying processes of collaborative governance. To unravel this black box, we explored how the authority of The Hague, The Netherlands, developed a programme tackling health inequalities drawing on a collaborative mode of governance. Methods: Case study drawing on qualitative semi-structured interviews and document review. Data were inductively analysed against the concept of collaborative governance. Results: The authority’s ambition was to co-produce a programme on tackling health inequalities with local actors. Three stages could be distinguished in the governing process: (i) formulating policy objectives, (ii) translating policy objectives into interventions and (iii) executing health interventions. In the stage of formulating policy objectives, the collaboration led to a reframing of the initial objectives. Furthermore, the translation of the policy objectives into health interventions was rather pragmatic and loosely based on health needs and/or evidence. As a result, the concrete actions that ensued from the programme did not necessarily reflect the initial objectives. Conclusion: In a local system of health governance by collaboration, factors other than the stated policy objectives played a role, eventually undermining the effectiveness of the programme in reducing health inequalities. To be effective, the processes of collaborative governance underlying area-based programmes require the attention of the local authority, including the building and governing of networks, a competent public health workforce and supportive infrastructures.