Food security depends on the resilience of agro-ecosystems, that is their capacity to withstand extreme climatic events. This depends upon above- and below-ground components of the ecosystem, yet a detailed understanding of how these different organisational levels will respond to perturbations is lacking. We describe a climatic perturbation of an ecosystem (a drought experiment conducted across large spatial scales in four bioclimatic regions) using three measures of stability to quantify the ecosystem’s response at three organisational levels (soil moisture, soil invertebrate community structure, and above-ground plant biomass). We found cascading effects of drought on these different organisational levels - while all three ecosystem components showed similar resistance to drought, soil moisture and soil invertebrates reached full recovery more often than plant biomass. Observed patterns suggest a strong interaction between biotic and abiotic pathways, translating into regional differences. We explore the consequence of these differences for agro-ecosystem resilience at large spatial scales.