That the Himalaya are warming at much higher rates than the global average is known. Here, we assess the future potential distribution of major plant communities in Sikkim Himalaya due to climate change using field observations and maximum entropy modelling approach. We collected data on presence and elevational distribution ranges of 584 endemic angiosperm species during field surveys at 121 sampling locations using 625 study plots and along an elevational gradient of 300–5,300 m. This field data was supplemented by already published records. Endemic species were classified into different growth forms, viz. trees, climbers, shrubs, and herbs. A total of 37,376 different species distribution models (SDMs) were built using climate projections available from 8 different general circulation models and 4 representative concentration pathways. SDMs were built for current climate (average climate for 1950–2000), 2050 (average climate for 2041–2060), and 2070 (average climate for 2061–2080). We found that about 16 and 18 % of endemic angiosperm species are likely to lose their potential habitat by 2050 and 2070, respectively. Meadows may likely lose about 1 and 3 % of their current geographical spread to shrublands by 2050 and 2070, respectively. Weak and insignificant values of phylogenetic signal among the growth forms indicated that climate-induced impacts were spread across the phylogenies. We report significant increase in the habitable areas of shrubs and their northward expansion, gradually replacing the herbaceous communities. This change can alter the structure and function of the Himalayan highland ecosystems besides depleting bioresource base and endangering the local livelihoods.