Agricultural systems in Europe face accumulating economic, ecological and societal challenges, raising concerns about their resilience to shocks and stresses. These resilience issues need to be addressed with a focus on the regional context in which farming systems operate because farms, farmers' organizations, service suppliers and supply chain actors are embedded in local environments and functions of agriculture. We define resilience of a farming system as its ability to ensure the provision of the system functions in the face of increasingly complex and accumulating economic, social, environmental and institutional shocks and stresses, through capacities of robustness, adaptability and transformability. We (i) develop a framework to assess the resilience of farming systems, and (ii) present a methodology to operationalize the framework with a view to Europe's diverse farming systems. The framework is designed to assess resilience to specific challenges (specified resilience) as well as a farming system's capacity to deal with the unknown, uncertainty and surprise (general resilience). The framework provides a heuristic to analyze system properties, challenges (shocks, long-term stresses), indicators to measure the performance of system functions, resilience capacities and resilience-enhancing attributes. Capacities and attributes refer to adaptive cycle processes of agricultural practices, farm demographics, governance and risk management. The novelty of the framework pertains to the focal scale of analysis, i.e. the farming system level, the consideration of accumulating challenges and various agricultural processes, and the consideration that farming systems provide multiple functions that can change over time. Furthermore, the distinction between three resilience capacities (robustness, adaptability, transformability) ensures that the framework goes beyond narrow definitions that limit resilience to robustness. The methodology deploys a mixed-methods approach: quantitative methods, such as statistics, econometrics and modelling, are used to identify underlying patterns, causal explanations and likely contributing factors; while qualitative methods, such as interviews, participatory approaches and stakeholder workshops, access experiential and contextual knowledge and provide more nuanced insights. More specifically, analysis along the framework explores multiple nested levels of farming systems (e.g. farm, farm household, supply chain, farming system) over a time horizon of 1–2 generations, thereby enabling reflection on potential temporal and scalar trade-offs across resilience attributes. The richness of the framework is illustrated for the arable farming system in Veenkoloniën, the Netherlands. The analysis reveals a relatively low capacity of this farming system to transform and farmers feeling distressed about transformation, while other members of their households have experienced many examples of transformation.