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Transdisciplinary research is increasingly used in projects dealing with transitions to sustainable, resilient and low-carbon societies. Transdisciplinary research projects require collaboration and coordination between researchers from different disciplinary backgrounds. Academic literature provides valuable insights on designing, facilitating, leading and evaluating transdisciplinary projects. While a substantial body of literature explores the challenges associated with transdisciplinary research, there is a scarcity of case studies exploring the challenges faced during different phases of project execution. In this paper we present a reflective account and analysis of our experiences during the first fifteen months of a transdisciplinary research project. The project is used as a case study, following a participatory action research methodology. Our findings verified the three types of challenge mentioned in the literature – inherent, institutional and teamwork related. This paper identifies a fourth type – emergent – that has not been discussed in the literature. Emergent challenges introduce uncertainty into TDR projects and are uncontrollable. Such challenges require research consortium leaders to develop adaptive strategies, and to take a mediation and leadership role in dealing with them. The article makes the following recommendations: emergent challenges require emergent strategies; funding should be more flexible to account for the nature of TDR research; TDR could be evaluated on the basis of its overall impact rather than on inflexible ‘deliverables’; academic publishing strategies must be incorporated into TDR projects; team development and co-location should be facilitated; and academic institutions should include performance and promotion criteria encouraging researchers to undertake roles in TDR projects. [ABSTRACT FROM AUTHOR]