Cities are faced with challenges to develop in ways that meet the increasingly urgent imperatives of planetary and population health. New approaches are needed to accelerate change, including innovative ways to influence policy makers through tailor-made and trust-based research-practice partnerships. The use of scientific evidence and participatory engagement is widely recognised today for its importance for complex policy processes of environmental public health. Trust relationships between scientists and cities practitioners within participatory research programmes is required. This work explores and analyses the evolution of the relationship between scientists and city practitioners formed during the CUSSH (Complex Urban System for Sustainability and Health) research programme, focused around a local case study, Rennes, in France. The results of the analysis demonstrate that, even if the primary objective of informing decision-making through evidence-based science is not fulfilled, the use of a decision-making support tool, a quantitative HIA in this case, may lay the foundations for trust relationships, in particular by facilitating the boundary between scientists and cities practitioners. To facilitate this process, it is essential to formalise the role of a boundary spanner and lay the conditions for iterative work between scientists and cities practitioners. Finally, the research highlights a set of necessary factors for efficient participatory research commonly cited in academic literature on science and policy interactions.