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Trees that characterized many agricultural landscapes across Europe are declining, despite the recent revival of agroforestry research and increasing direct payments for their maintenance. Therefore, in addition to field experiments, there is a need for transdisciplinary research in close alliance with local farmers. This paper proposes a three-step participatory design and assessment approach, incorporating local innovation and scientific evidence. To our knowledge, this is the first participatory and bioeconomic analysis of farmer-designed agroforestry systems in Europe. First, an exploratory survey of farmers' innovations in Switzerland was conducted together with a literature review. Based on the survey, 14 representative agroforestry practices were defined for the bioeconomic assessment, focusing on walnut ( Juglans hybr.) and wild cherry ( Prunus avium) . The predictions of long-term yields were made with the Yield-SAFE model, and the profitability was assessed using the Farm-SAFE model. The survey results suggested a lack of local knowledge on key ecosystem services provided by agroforestry. It is therefore recommended to apply the concept of ecosystem services, in order to support the design of multifunctional agriculture and to increase the willingness to pay for its services. According to our yield predictions, mixing trees and crops was commonly more productive (12 out of the 14 options, land equivalent ratio = 0.95-1.30) than growing them in separate forestry or arable systems. This result contradicts the widespread view among modern Swiss farmers that agroforestry is unproductive. In terms of profitability, 68 % of the 56 financial scenarios for the agroforestry practices, particularly those linked to innovative marketing of fruit or receiving payments for ecosystem services, were found to be more profitable than the business as usual reference systems. These results demonstrate that there is a need and a value in bridging the gap between scientists and farmers, in order to coproduce applied knowledge for the design of productive agroforestry practices. [ABSTRACT FROM AUTHOR]