Integrated crop–livestock systems are often considered a promising way to address agricultural sustainability issues. Many authors claim that complementarities and synergies between crops and livestock can improve nutrient cycling and delivery of ecosystem services (ES) in agricultural systems. They have analyzed effects of interactions at the farm level and affirmed the potential advantage of developing crop–livestock interactions at the territory level. However, potential benefits of developing synergies beyond the farm level have not been clearly identified. Thus, we developed a conceptual framework that can be used to analyze, design and perform integrated assessment of crop–livestock systems at the territory level. To address crop–livestock interaction issues, we define it as a social-ecological system called the territorial crop–livestock system (TCLS). The ecological system is represented as three interacting components, crops, grasslands and animals, allowing description of various land uses and their potential effects on nutrient cycling and ES. The social system, represented as farmers interacting with natural-resource managers and agro-food chain actors, determines land use and the nature and intensity of ES delivered. We highlight the importance of coordination and learning among actors to support implementation of complex adaptive systems such as TCLSs. We illustrate the expressive power of our conceptual framework through development of a generic typology of crop–livestock systems. Then we show how our conceptual framework can be used as an intermediary object with stakeholders in participatory design approaches. We illustrate this process by representing four archetypal TCLSs. We provide an example of the design approach implemented in Southwestern France to address severe recurrent water shortages, which includes analysis of land use in the current crop–livestock system and the associated key metabolic and ES issues, identification of options for change and multi-criteria analysis of these options. We conclude that this framework shows great potential to support development of sustainable farming systems at the territory level.