Understanding the vegetation and soil ecology of natural habitats harbouring threatened species is critical in conservation planning and restoration. The present study investigated the vegetation composition and soil physico‐chemical properties of natural habitats of Trillium govanianum – a threatened Himalayan endemic species. We laid 120 quadrats across eight randomly selected sites where the species was growing in the Kashmir Himalaya. We collected the soil samples from these sites and determined soil physico‐chemical properties using standard methods. Across all the sites, we found a total of 57 plant species with dominance of Rosaceae and Ranunculaceae. The importance value index (IVI) results revealed that Fragaria nubicola, Corydalis diphylla, Galium aparine, and Leucanthemum vulgare, were the dominant species in T. govanianum habitats. The density, abundance and IVI of three‐leaf vegetative plants was higher than one‐leaf vegetative and three‐leaf reproductive plants across all the study sites. We found that T. govanianum alone forms 23.5% positive, 0 negative, 76.4% random co‐occurrences with other associated species in its habitats. Our results reveal that the variations in vegetation composition among the sites was influenced by differences in soil properties. Principal component analysis (PCA) revealed that several soil properties such as organic carbon (OC), nitrogen, potassium, and sulphur were concentrated in five sites, namely Dara, Drung, Bangus, Gulmarg and Doodhpathri, which also showed the highest density, frequency, and abundance of T. govanianum. Overall, our study contributes quantitative information on the vegetation and soil ecology of T. govanianum‐habitats, which in turn can help in developing conservation strategies for this threatened species, and its sustainable management and habitat restoration.