Climate change impacts on vegetation are mediated by soil processes that regulate rhizosphere water balance, nutrient dynamics, and ground-level temperatures. For ecosystems characterized by high fine-scale substrate heterogeneity such as grasslands on poorly developed soils, effects of climate change on plant communities may depend on substrate properties that vary at the scale of individuals (<m2), leading to fine-scale shifts in community structure that may go undetected at larger scales. Here, we show in a long-running climate experiment in species-rich limestone grassland in Buxton, England (UK), that the resistance of the community to 15-year manipulations of temperature and rainfall at the plot scale (9 m2) belies considerable community reorganization at the microsite (100 cm2) scale. In individual models of the abundance of the 25 most common species with respect to climate treatment and microsite soil depth, 13 species exhibited significant soil depth affinities, and nine of these have shifted their position along the depth gradient in response to one or more climate treatments. Estimates of species turnover across the depth gradient reviewed in relation to measurements of water potential, nitrogen supply, pH, and community biomass suggest that communities of shallow microsites are responding directly to microenvironmental changes induced by climate manipulation, while those of the deepest microsites are shifting in response to changes in competitive interference from more nutrient-demanding species. Moreover, for several species in summer drought and winter heated treatments, climate response in deep microsites was opposite that of shallow microsites, suggesting microsite variation is contributing to community stability at the whole-plot level. Our study thus demonstrates a strong link between community dynamics and substrate properties, and suggests ecosystems typified by fine-scale substrate heterogeneity may possess a natural buffering capacity in the face of climate change.