Abstract Sustainable intensification of agriculture requires the adoption of new production techniques, tools, and programmes on a large scale. This implies substantial shifts in established ways of farming under uncertain information about potential economic and environmental outcomes. Research can support stakeholders such as farmers, industry, and policy in this transformation by providing evidence-based information. The provision of such information can be improved by combining ex-ante and ex-post assessment tools at different stages of policy cycles and projects. We here present a unique combination of ex-ante bio-economic modelling analysis and ex-post econometric analyses based on survey data using the example of a novel pesticide-free wheat production programme in Switzerland. We exemplify how ex-ante and ex-post evaluation can be combined to increase the robustness of results for stakeholders, e.g. on yield losses from pesticide-free production or farmer typologies important for adoption. Further, we show how their alignment can improve future assessments in project and policy cycles, e.g. through the choice of suitable variables explaining farmer decision-making and priors on the distribution of their characteristics. Despite the identified synergies between assessments, we also find that their integration is limited by the timing and information requirements of stakeholders at different stages in the project. Finally, potential synergies in our case study strongly depended on the type of ex-ante models chosen for evaluation and their alignment with ex-post methods. Especially integrating farmer behaviour in ex-ante assessments seems to be crucial to arriving at holistic evaluations of large-scale programmes for sustainable agricultural practices and providing useful information to stakeholders.