Finding pathways to more sustainability and resilience of farming systems requires the avoidance of exceeding critical thresholds and the timely identification of viable alternative system configurations. To serve this purpose, the objective of this paper is to present a participatory, integrated and indicator-based methodology that leads researchers and farming system actors in six steps to a multi-dimensional understanding of sustainability and resilience of farming systems in the future. The methodology includes an assessment of current performance (Step 1), identification of critical thresholds whose exceedance can lead to large and permanent system change (Step 2), impact assessment when critical thresholds are exceeded (Step 3), identification of desired alternative systems and their expected improved performance of sustainability and resilience (Step 4), identification of strategies to realize those alternative systems (Step 5), and an assessment on the compatibility of alternative systems with the developments of exogenous factors as projected in different future scenarios (Step 6). The method is applied in 11 EU farming systems, and the application to extensive sheep production in Huesca, Spain, is presented here, as its problematic situation provides insights for other farming systems. Participants in the participatory workshop indicated that their farming system is very close to a decline or even a collapse. Approaching and exceeding critical thresholds in the social, economic and environmental domain are currently causing a vicious circle that includes low economic returns, low attractiveness of the farming system and abandonment of pasture lands. More sustainable and resilient alternative systems to counteract the current negative system dynamics were proposed by participants: a semi-intensive system primarily aimed at improving production and a high-tech extensive system primarily aimed at providing public goods. Both alternatives place a strong emphasis on the role of technology, but differ in their approach towards grazing, which is reflected in the different strategies that are foreseen to realize those alternatives. Although the high-tech extensive system seems most compatible with a future in which sustainable food production is very important, the semi-intensive system seems a less risky bet as it has on average the best compatibility with multiple future scenarios. Overall, the methodology can be regarded as relatively quick, interactive and interdisciplinary, providing ample information on critical thresholds, current system dynamics and future possibilities. As such, the method enables stakeholders to think and talk about the future of their system, paving the way for improved sustainability and resilience.