One of the most crucial steps in the practical conservation of endangered endemic mountain plants is to address their population size status and habitat requirements concurrently with understanding their response to future global warming. Three endangered Silene species—Silene leucophylla Boiss., S. schimperiana Boiss., and S. oreosinaica Chowdhuri—in Egypt were the focus of the current study. These species were examined for population status change, habitat quality variables (topography, soil features, and threats), and predictive current and future distributions. To find population size changes, recent field surveys and historical records were compared. Using Random Forest (RF) and Canonical Correspondence Analysis (CCA), habitat preferences were assessed. To forecast present-day distribution and climate change response, an ensemble model was used. The results reported a continuous decline in the population size of the three species. Both RF and CCA addressed that elevation, soil texture (silt, sand, and clay fractions), soil moisture, habitat-type, chlorides, electric conductivity, and slope were among the important variables associated with habitat quality. The central northern sector of the Saint Catherine area is the hotspot location for the predictive current distribution of three species with suitable areas of 291.40, 293.10, and 58.29 km2 for S. leucophylla, S. schimperiana, and S. oreosinaica, respectively. Precipitation-related variables and elevation were the key predictors for the current distribution of three Silene species. In response to climate change scenarios, the three Silene species exhibited a gradual contraction in the predictive suitable areas with upward shifts by 2050 and 2070. The protection of these species and reintroduction to the predicted current and future climatically suitable areas are urgent priorities. Ex-situ conservation and raised surveillance, as well as fenced enclosures may catapult as promising and effective approaches to conserving such threatened species.