Land use has a great impact on soil dynamics. The soils of various land use systems in Central Karakoram have been under immense pressure in the recent past due to certain anthropogenic activities such as land use practices and land use cover changes. These influences have an impact on the spatial distribution of metallic elements (MEs) in the soils of various land uses. Herein, we investigated the occurrence of the MEs, copper (Cu), zinc (Zn), and nickel (Ni), in soils of various land uses such as the permafrost, pasture, forest, and agricultural lands of the Central Karakorum region. The MEs were extracted in exchangeable, adsorbed, organically bound, carbonated, precipitated, and residual forms. The concentrations of MEs showed a significant dependence on the extraction method used, and the extraction trend followed the order of EDTA > HNO3 > KNO3 > NaOH > H2O. Zn showed the highest concentration compared to Ni and Cu in all extractions, whereas the land uses’ ME concentration followed the order of agricultural land > permafrost > forest > pasturelands. The highest values of total Zn, Ni, and Cu were 712 ± 01 mg/kg, 656 ± 02 mg/kg, and 163 ± 02 mg/kg, respectively, in agricultural soil. The ME concentration showed significant variations between different land uses, and the highest concentration was noted in agricultural soil. Zn was found to be a dominant ME compared to Ni and Cu. We believe this effort will provide opportunities for scholars to investigate MEs around the globe.