Small agricultural firms have to cope with increasing economic, legal and environmental difficulties. The purpose of the paper is to identify whether there are available research outputs to these challenges, focusing on the Swiss traditional fruit sector. Identification of firms’ needs using face-to-face interviews and a focus group allowed us to prioritize innovations. Knowledge and innovation transfer gaps were identified thanks to bibliometric analysis, providing hints for research program orientations. The main sectoral needs were related to varieties like increasing pest and disease resistance, weather sensitivity, and ripening behavior. Knowledge produced by research institutions was partly related to the firms’ needs. The study demonstrated a need for better coordination between agricultural stakeholders and researchers. Knowledge must be transferred and shared in the network with greater efficiency by extending interactions and involving stakeholders earlier in the innovation process. However, the search for scientific outputs should include more specificities of the local environment.