This report outlines recommendations for science policy regarding biodiversity and pandemics that need to be implemented in order to develop broader transformative policies for human, animal, and ecosystem health. In particular, we focus on policies to support and promote research needed to better prevent and manage spillover events in which pathogens originating in wildlife cause disease outbreaks or even pandemics in humans or large-scale disease events in domesticated animals (panzootics). The report was prepared by an Eklipse Expert Working Group (EWG) active from 2022-2023. The EWG consisted of scientists with relevant expertise in the natural, biomedical, and social sciences. The group undertook a scoping review of scientific literature and collected input from a large body of external experts through an online survey and focus group discussions. Using these results, the EWG formulated recommendations for shaping a strategic research agenda on biodiversity and pandemics. These recommendations address the critical interlinkages between relevant sectors and stakeholders via targeted transdisciplinary research to make future actions more effective. Crucially, in the following recommendations we call for moving beyond incremental changes to science policy and bringing about transformative change to how research is carried out, organised, and financed. Only in this way will science itself deliver the knowledge and insights needed to develop policies that will help transform human animal and ecosystem health, avoiding the accumulation of problems generated by the still widespread business as usual approach to both research and broader policymaking. Our ability to deliver this transformative change is essential to confront other global crises, including the climate and biodiversity crises, that are currently threatening our societies.