In developed countries, the development of interactions between crops and livestock could enhance sustainability of agriculture, as an alternative to the specialization trends. Strengthening integration of crop and livestock at farm and territory levels may improve metabolism efficiency of agricultural systems and enhance ecosystem services. It also allows diversifying income sources and creating activities locally. To design such Integrated Crop-Livestock Systems (ICLS), the socio-economic contexts must be taken into account to overcome sociotechnical lock-in, through situated co-design with stakeholders. We present in this article a participatory approach to design ICLS at farm and territory levels in the Aveyron river watershed (South-West France). In this highly diversified area coexist irrigated or nonirrigated arable farming systems in lowlands and more or less intensive livestock systems in upper lands. With local stakeholders (farmers, land and water resources managers, environmental associations, collect and storage organisms, agricultural advisors) we built a diagnosis of local croplivestock integration challenges and issues, identified the existing interactions and imagined promising options of integration. These options were articulated in two scenarios: a “territorial integration” scenario referring to large flows of products between lowlands and highlands, a “collective-level integration” scenario referring to small groups of farmers exchanging products and collaborating in a flexible way. These two scenarios have been discussed and assessed using a multicriteria assessment based on the participative diagnosis. Through our assessment and design participatory approach, stakeholders identified and described different ways for sustainable crop-livestock integration based on the local biophysical and social resources and the diversity of farming systems. At territorial level, integration would occur through collaboration between crop-specialized areas producing alfalfa for livestock areas. This collaboration would be driven by cooperatives and set on a large scale. At collective level, integration would occur through collective organisation and informal agreements between farmers, animated and organised by a farmers’ association. The combination of both approaches is discussed as an opportunity for deep crop-livestock integration and transition in farming practices towards more agroecological practices.