Abstract Context Predicting how changes in weather patterns and land use jointly impact populations is a pressing task in ecology. Microclimate may play a key role in species’ local persistence by modulating regional weather effects. We lack sufficient empirical evidence to understand the relative effects of landscape structure and habitat conditions on intraspecific trait variation. Objectives Using a spatially and temporally replicated demographic dataset, we tested the relative effect of landscape structure (area and connectivity of remnant habitat fragments), microclimate (heat load), and fluctuation in weather conditions (study year) on intraspecific plant trait variation, and we investigated whether the local heat load modulated the weather effects on the studied traits. Methods We performed repeated measurements of stem height, leaf area, number of stems, main inflorescence length and number of primary side inflorescences of 569 permanently marked individuals of the grassland specialist Salvia nemorosa L. We sampled 13 populations encompassing microhabitats exposed to different heat load levels, over three consecutive years. Results Mature individuals had fewer stems in isolated, and taller stems in small habitat fragments. High levels of heat load and dry years affected negatively all measured traits, and the negative effects of exposure to high heat load were generally exacerbated in dry years. Conclusions Exposure to strong environmental stressors could ultimately obscure the real effect of human impact on plant populations. Landscape planning for conservation of dry grassland species should ensure not only improved habitat connectivity but also high-quality habitats with heterogeneous microclimates able to buffer weather extremes.