Climate change is projected to increase flood risks in western Africa. In the FANFAR project, a pre-operational flood early warning system (FEWS) for western Africa was co-designed in workshops with 50–60 stakeholders from 17 countries, adopting multi-criteria decision analysis (MCDA). We aimed at (i) designing a FEWS with western African stakeholders using MCDA and (ii) evaluating participatory MCDA as a transdisciplinary process. To achieve the first aim (i), we used MCDA methods for problem structuring and preference elicitation in workshops. Problem structuring included stakeholder analysis, creating 10 objectives to be achieved by the FANFAR FEWS and designing 11 possible FEWS configurations. Experts predicted FEWS configuration performance, which we integrated with stakeholder preferences. We tested MCDA results in sensitivity analyses. Three FEWSs showed good performance, despite uncertainty, and were robust across different preferences. For stakeholders it was most important that the FEWS produces accurate, clear, timely, and accessible flood risk information. To achieve the second aim (ii), we clustered common characteristics of collaborative governance frameworks from the sustainability science and transdisciplinary literature. Our framework emphasizes issues crucial to the earth systems sciences, such as uncertainty and integrating interdisciplinary knowledge. MCDA can address both well. Other strengths of MCDA are co-producing knowledge with stakeholders and providing a consistent methodology with unambiguous, shared results. Participatory MCDA including problem structuring can contribute to co-designing a project but does not achieve later phases of transdisciplinary processes well, such as co-disseminating and evaluating results. We encourage colleagues to use MCDA and the proposed framework for evaluating transdisciplinary hydrology research that engages with stakeholders and society.