PREMISE Understanding edaphic specialization is crucial for conserving rare plants that may need relocation due to habitat loss. Focusing on Eriogonum crosbyae, a rare soil specialist in the Great Basin of the United States, we asked how site‐level variation among volcanic soil outcrops affected plant growth and population distribution. METHODS We measured emergence, survival, size, and biomass allocation of E. crosbyae seedlings planted in soils collected from 42 outcrops of actual and potential habitat. We also measured phenotypic variation in the wild, documented abiotic and biotic components of E. crosbyae habitat, re‐surveyed Nevada populations, and evaluated occupancy changes over time. RESULTS Plants responded plastically to edaphic variation, growing larger and allocating relatively more to aboveground tissues in soils with greater nutrient availability and growing smaller in soils higher in copper in the field and the greenhouse. However, the chemical and physical soil properties we measured did not predict site occupancy, nor was plant phenotype in the greenhouse different when plants were grown in soils from sites with different occupation status. We observed occupation status reversals at five locations. CONCLUSIONS Eriogonum crosbyae performed well in soils formed on hydrothermally altered rocks that are inhospitable to many other plants. Extirpation/colonization events observed were consistent with metapopulation dynamics, which may partially explain the patchy distribution of E. crosbyae among outcrops of potential habitat. While soil properties did not predict site occupancy, early life stages showed sensitivity to soil variation, indicating that seedling dynamics may be important to consider for the conservation of this soil specialist.