Phoebe bootanica (Meisn.) M. Gangop., an endemic evergreen tree species of the Indo-Myanmar biodiversity hotspot, faces significant threats due to overexploitation and habitat fragmentation, necessitating urgent conservation efforts. This study investigates the population structure and regeneration status of P. bootanica across its natural distribution in North-eastern India to inform conservation strategies under the projected climate change. Sporadic field surveys conducted from April 2021 to October 2023 across five states employed purposive cum random sampling in 0.1-hectare plots to assess morphological traits (height, girth, basal area, clear bole height, and bark thickness) and density of P. bootanica and associated tree species. Regeneration status was evaluated based on seedling, sapling, and adult counts, while girth class distribution provided insights into population dynamics; both indicate the reproductive fitness of the species in natural populations. The Kruskal–Wallis test revealed significant variations in morphological traits across sites, with Sorbung exhibiting the highest mean girth (357.08 ± 197.63 cm) and basal area (13.00 ± 11.59 m²/ha). Regeneration was generally poor, with most sites showing limited evidence of seedlings and saplings, indicating challenges in natural recruitment, possibly due to the species’ recalcitrant seeds and shade-dependent regeneration. High timber demand has fragmented populations, contributing to its endangered status (IUCN B2ab(iii)). This study underscores the need for targeted conservation, including in situ and ex situ strategies, to enhance genetic diversity and population resilience. Our findings provide a baseline for long-term monitoring and sustainable management of the species, emphasizing the integration of community-level conservation initiatives to safeguard this ecologically and commercially significant species. Ecological Niche Modelling (ENM) is recommended to identify suitable habitats for future conservation planning in the projected climate change.