Alternative technologies development in sustainability transition require stakeholders’ joint-commitment for strategic system building, in order to reverse the lock-in prevailing in most sectors. Among the various strategic system building modes, this article focuses on the role of production contracts in value chains, as a networking lever for system building. If contracting has been studied in innovation economics, notably for R&D contracts or license contracts, there is a lack of evidence on how contracting for goods may also favor joint-knowledge development particularly for alternative goods in less technological intensive sectors. Based on a combination of Transaction Costs Economics, Relational-View of Strategic Management and Technological Innovation System literature, we propose an original analytical framework to disentangle the micro-mechanisms by which production contract governance (PCG) in value chains can be considered as strategic networking lever for system-building. We apply this framework to six case studies in European agricultural value-chains engaged in developing legumes, being alternative crops of high interest for both agricultural and food sustainability. Main results show that PCG between farmers, intermediary organizations and processors foster network structural and human resources that help alternative agricultural value-chain structuration. Those insights are particularly interesting for practitioners and policy makers to support PCG as a networking lever for alternative agri-food chains development; but they also offer new research agenda to analyze the role of PCG in other sectors in transition.