With the concept of resilience being increasingly applied in farming systems research, there is general agreement that the resilience theory should be supported by sound assessment methodologies. Yet, in the extant literature, definitions and measures of resilience as a system outcome, a system capability or a process are often conflated, causing conceptual and methodological ambiguities. To overcome these limitations, here we systematically review the literature on assessing the resilience of farming systems and identify patterns, including similarities and differences in underpinning theories and in methodologies. We analyzed 123 papers on how the resilience of farming systems is conceptualized and assessed. From these papers, we identified four theoretical positions (“lenses”): traditional, vulnerability, capacities, and agroecology. These lenses differ and complement each other in terms of the outcome definition of resilience (stability, transformation, and reduced vulnerability), the prominent components of resilience (capacities, practices, and resources), and the perturbations that farming systems are exposed to (shocks, exposure, and sensitivity). Collectively, these lenses offer a novel causality framework with a complementary set of causal links between perturbations, components, and outcomes. This paper suggests for the first time that resilience assessment methodologies can be further developed by drawing from the strengths and complementarities of the different perspectives. Hence, this paper identifies five design choices that need to be made in order to rigorously assess the resilience of farming systems. These concern the choice of system traits, of perturbations, of type of resilience, of contributing factors, and of resilience outcomes that will be considered.