Climate change threatens the persistence of native plants across California, and strategies are needed to facilitate resilience and conserve the most vulnerable species. Conserving species under climate change is complicated, however, because the state’s native flora are threatened by other global changes, including altered disturbance regimes, land use change, and invasive species. We developed an integrated modeling framework to assess the relative impacts of multiple threats, and to rank management responses, for five endemic plant species in southern California. The modeling framework integrates land use change projections with projected species’ distribution shifts under climate change, which are subsequently linked to a stochastic population model. The population model predicts plant species persistence under alternative habitat change scenarios in addition to different fire regime and management scenarios. Overall, climate change was projected to produce large changes in species’ suitable habitat, although these changes varied by species and climate change scenario. Despite projections of large habitat shifts under climate change, too-frequent fire was the top-ranked threat for most species. Urban development often exacerbated habitat loss under climate change, but the relative impact on species’ persistence was largely a function of where the species is located on the landscape. In conclusion, if climate change impacts on species can be implied through altered distribution patterns, large changes can be expected in southern California. However, management strategies to address these habitat shifts would most likely not be effective unless other threats, particularly increased fire frequency, are not accounted for.