Agricultural systems are complex, because managers need to cope with interlinked and dynamic ecological, social, political and economic aspects. Understanding and analysing such systems requires researchers to adopt a holistic approach to grasp the links between those aspects. Holistic approaches within agricultural research – known as Farming Systems Research (FSR) support researchers in sharing knowledge and different perspectives concerning the research process and problems. Sharing knowledge and perspectives enables to holistically understand and conceptualise complex systems, as well as to structure and manage research projects. The aim of this paper is to suggest and present a guideline for agricultural researchers to carry out an economic and environmental analysis of food supply chains with a FSR approach. We describe how participants of the EU-project SOLIBAM (Strategies for Organic and Low-input Integrated Breeding and Management) used the guideline to structure, manage and carry out an economic and environmental analysis of the food supply chains of concern. The FSR approach enabled the participants to jointly define and model the structure of the supply chains, identify the requirements for data collection and collect data.