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Boosting the productivity of smallholder farming systems continues to be a major need in Africa. Challenges relating to how to improve irrigation are multi‐factor and multisectoral, and they involve a broad range of actors who must interact to reach decisions collectively. We provide a systematic reflection on findings from the research project EAU4Food, which adopted a transdisciplinary approach to irrigation for food security research in five case studies in Ethiopia, Mali, Mozambique, South Africa and Tunisia. The EAU4Food experiences emphasize that actual innovation at irrigated smallholder farm level remains limited without sufficient improvement of the enabling environment and taking note of the wider political economy environment. Most project partners felt at the end of the project that the transdisciplinary approach has indeed enriched the research process by providing different and multiple insights from actors outside the academic field. Local capacity to facilitate transdisciplinary research and engagement with practitioners was developed and could support the continuation and scaling up of the approach. Future projects may benefit from a longer time frame to allow for deeper exchange of lessons learned among different stakeholders and a dedicated effort to analyse possible improvements of the enabling environment from the beginning of the research process. © 2020 The Authors. Irrigation and Drainage published by John Wiley & Sons Ltd on behalf of International Commission for Irrigation and Drainage