Colchicum luteum is currently a rare and threatened medicinal plant species in the Kashmir Himalaya. Due to the subsequent increase in anthropogenic pressure on medicinal plant species, it is imperative to understand the phytosociological and conservational status of the plant in its natural habitat. The objectives of this study were analysed in year 2018–2019 on the phytosociological data, viz. density, frequency, and abundance, as well as the rhizospheric soil microbial diversity of C. luteum in disturbed and undisturbed areas of the Kashmir Himalaya. We examined the distribution pattern, phytosociological data, and conservation status of C. luteum by analysing ecological features like abundance, frequency, and density in all three selected locations in Kashmir, Northern India and were found maximum values at Undisturbed areas. The highest values of density (3.24 ± 0.69 m2), frequency (57.77 ± 13.55%), and abundance (5.49 m2) were recorded at undisturbed site Harwan. The total bacterial count (CFU) and Vesicular Arbuscular Mycorrhiza (VAM) spore population from the rhizospheric soil of C. luteum were also analysed, with higher bacterial count i.e., Pseudomonas, Azatobacter, Rhizobium and PSB were (26.2 ± 0.648) (21.88 ± 0.675) (30.11 ± 0.576) and (14.11 ± 0.671) and VAM spore population (g−1) of soil recorded 6.36 ± 0.550 at undisturbed areas viz. Harwan. The bacteria and fungi are likely keystone organisms that form an interface between soils and plant roots. Mutualistic associations with host plants have been observed in various natural and agricultural ecosystems. The present findings could be helpful in formulating conservation strategies for C. Luteum threatened and endangered medicinal plant present in North western Himalayan regions. The plant in disturbed areas that are affected by anthropogenic activities like tourism, grazing, deforestation, urbanization, transport etc. impacts on phytosociological and soil microbial patterns in the area. Because of these abiotic pressures, causes a reduction in plant cover in forest regions, soils become exposed, affecting soil microbial health. Therefore, the study shows the necessity for best practices for medicinal plant and forest management that provide effective monitoring and regulation of human activities in the offshore forest regions and avoid the intrusion of existing reserves. © 2022 The Author(s)