This paper studies knowledge production in complex, collaborative research projects that brought together academics from different disciplines, research users and agricultural businesses. It takes a comparative approach, studying the interactions within interdisciplinary research teams from ten case studies, considering the process of collaboration from initial idea through to publication. The research developed a typology of participants in these projects, and identified the motivations and challenges of each. Our results analyse the process of research teams coming together and the relationships that are built up during the research. A particular challenge identified was the building of cooperation and trust. This issue is explored alongside issues of communication, methodology, data analysis and the process of drawing and publicising conclusions.