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It is typically assumed that for species to persist in working landscapes, they must either persist alongside agricultural pressures (i.e. land-sharing) or become restricted to remnant patches of natural habitat (i.e land-sparing). However, a third possibility is that species survive in stable ecological refuges that then supply the surrounding matrix with immigrants. In this study, we examined the potential for refuge-colonisation dynamics across two Key Biodiversity Areas dominated by commercial farmland in South Africa. We combined six years of remote sensing and two years of field surveys to examine mountains and rocky outcrops as ecological refuges using butterflies as indicators of environmental change. Vegetation on mountains and outcrops had higher and less variable productivity and moisture retention than the matrix, even across exceptionally wet and dry years. Moreover, butterflies in the matrix were a nested subset of species from the mountains and outcrops, and there was little evidence that species with certain traits were limited to either habitat. This suggests that species can retreat to ecological refuges during harsh conditions and recolonise the surrounding matrix once conditions improve. Ecological refuges can, therefore, unify land-sharing and land-sparing because their targeted protection would support the persistence of species throughout wider landscapes.