In an era of climate change, identifying suitable habitats for ecosystem restoration is critical for conservation of globally threatened biodiversity. Here, we integrate the insights gained from ensemble modelling with the community ecology data on threatened Himalayan Trillium (Trillium govanianum) to identify the suitable sites for its habitat restoration. We used ensemble modelling to map the current potential distribution and predict the future suitable habitats for the species under future climate change scenarios. The predictive accuracy of the ensemble model was fairly good; and the most influential variables governing the distribution of Himalayan Trillium were precipitation of the driest month followed by mean diurnal range. The current potential suitable habitats for this species are mostly located in western parts of the Himalaya; however, a range shift from western to eastern Himalaya is predicted under future climate change scenarios. Further, the results of community data revealed that Himalayan Trillium is positively associated with two tree species (Abies pindrow and Taxus wallichiana) forming forest top-story, four understory shrubs (Viburnum grandiflorum, Parrotiopsis jacquemontiana, Skimmia laureola and Rhododendron campanulatum) and one herbaceous species (Podophyllum hexandrum). In particular, the shrubs serve as natural micro-refuges by facilitating the suitable growth and protect the species from unsustainable extraction and livestock grazing. Our findings highlight a two-pronged strategy for habitat restoration of Himalayan Trillium: (i) identification of suitable habitats using ensemble modelling at the pan-Himalayan scale, (ii) and its integration with the community information at local scale. Such an integrated approach offers a nature-based solution in guiding the climate change-integrated restoration programs in the Himalaya, and elsewhere in the world.