Tools and methodologies have been developed to enable integrated analysis (IA) of complex issues like agro‐ecosystems and natural resources management. They are based on interdisciplinary and often on participatory approaches combining, interpreting and communicating knowledge from diverse scientific disciplines and from stakeholders. In this paper we present the original educational programme built to enable students in agronomy to implement participatory IA methods in order to deal with sustainability issues in rural territory. In this educational programme students take a professional project management situation on a given case study. One of the originality of the course programme lies in its twofold objectives: building student capacities for carrying out integrated multi‐scale analysis of complex systems and providing researchers with an operational research device which facilitates the integrated analysis of new study territories. The educational programme articulates trips in the case study region and formation modules on project management, farming systems sustainability assessment, landscape multifunctionality analysis, stakeholder analysis and interviews, territorial diagnosis and narrative scenario construction. The main objectives and methods used in these modules are presented and discussed in the light of the outcomes of the implementation of this educational programme. Discussion is focused on the main educational and research issues of this programme.