Land use has a greater impact on trace element (TE) concentration present in soils. In mountainous regions of the western Himalayas, some dominating geogenic and human-dependent anthropogenic factors are involved in the spatial distribution of TEs in various land uses. Soil samples were collected from permafrost, pasture, forest, and agricultural land-use systems of Babusar Valley and Fairy Meadows in Diamer districts and the Rama region in Astore Districts in replications for investigation of three TEs, i.e., copper (Cu), zinc (Zn), and nickel (Ni). These samples were analyzed for exchangeable, adsorbed, organically bound, carbonate precipitated, and residual forms. Significant differences among these TEs were observed. Differences in the levels of TEs within soil samples were observed to be influenced by land usage patterns. The physicochemical properties of soil samples were also investigated. Additionally, the total metals (Ni, Zn, Cu) were extracted and their concentrations were measured in all samples. The concentration of soil TEs was observed in the following order: adsorbed < organically bound < exchangeable < residual < carbonate precipitated form across all the land uses. The results indicate that the contents of TEs (Ni, Zn, Cu) in agricultural soils were greater than in the permafrost pasture and forest soil samples. The total TE concentration varied as Zn > Ni > Cu irrespective of the area and land uses. We believe this work will open avenues for researchers to explore TEs in various regions of the world.