Juniperus macropoda is the only tree species of a cold desert ecosystem that is experiencing high anthropogenic pressure and has a poor regeneration status due to harsh environmental conditions. Due to the limited distribution of Juniperus macropoda in this region, the species have remained largely unexplored in terms of understanding the distribution pattern along the elevation and soil fertility gradients. Therefore, the current research was carried out along the elevational gradient, starting from the base line at 3000 m above sea level (m asl) asl with an elevational plot distance of 180 m. The study revealed that the average density of J. macropoda declined gradually from the first elevation range, i.e., 3000–3180 m asl onward, and extended up to the elevation range of 3900–4080 m asl. However, the average seedling and sapling densities were highest at mid-elevation and extended up to an elevation range of 4080–4260 m asl. The J. macropoda population formed a reverse J-shaped structure only up to 3540–3720 m asl. The maximum total biomass and carbon density were recorded in the lowest elevational range, and decreased subsequently. The primary soil nutrients under study decreased sharply along the elevational gradient. Seedling, sapling and tree distributions had a significantly positive relationship (p < 0.05) with available N, P, K, SOC, silt and clay contents and were negatively correlated (p < 0.05) with sand contents. The outcome of the study will form the basis for devising a plan for the management and conservation of J. macropoda forests.