Climate change is reorganizing the planet's biodiversity, necessitating proactive management of species and habitats based on spatiotemporal predictions of distributions across climate scenarios. In marine settings, climatic changes will predominantly manifest via warming, ocean acidification, deoxygenation, and changes in hydrodynamics. Lophelia pertusa, the main reef‐forming coral present throughout the deep Atlantic Ocean (>200 m), is particularly sensitive to such stressors with stark reductions in suitable habitat predicted to accrue by 2100 in a business‐as‐usual scenario. However, with new occurrence data for this species along with higher‐resolution bathymetry and climate data, it may be possible to locate further climatic refugia. Here, we synthesize new and published biogeographic, geomorphological, and climatic data to build ensemble, multi‐scale habitat suitability models for L. pertusa on the continental margin of the southeast United States (SEUS). We then project these models in two timepoints (2050, 2100) and four climate change scenarios to characterize the occurrence probability of this critical cold‐water coral (CWC) habitat now and in the future. Our models reveal the extent of reef habitat in the SEUS and corroborate it as the largest currently known essentially continuous CWC reef province on earth, and also predict abundance of L. pertusa to identify key areas, including those outside areas currently protected from bottom‐contact fishing. Drastic reductions in L. pertusa climatic suitability index emerged primarily after 2050 and were concentrated at the shallower end (<~550 m) of the regional distribution under the Gulf Stream main axis. Our results thus suggest a depth‐driven climate refuge effect where deeper, cooler reef sites experience lesser declines. The strength of this effect increases with climate scenario severity. Taken together, our study has implications for the regional and global management of this species, portending changes in the biodiversity reliant on CWC habitats and the critical ecosystem services they provide.