The contamination of soil by toxic metal(oid)s has emerged as a major concern worldwide, particularly in developing countries. A metals behavior in the soil environment is influenced by organic matter, mineral phases, and oxidation states in which a particular metal exists. However, the spectroscopic evidence of metal(oid)s interactions in soil with organic matter and mineral phases can induce an extensive understanding. The surface and sub-surface soils (0-50 cm) from four sites of upper Indus basin, Pakistan, were collected and analyzed by using FTIR (Fourier-transform infrared spectroscopy), XRD (X-ray diffraction) and XPS (X-ray photoelectron spectroscopy) in addition to ICP-MS (inductively coupled plasma mass spectrometry) and geochemical fractionation. Geochemical fractionation of metal(oid)s indicated that As, Cu, Ni, Pb, and Zn were mostly found in the potentially bioavailable fractions. However, an increase in the residual fraction was observed from top to bottom. The absorption bands of FTIR spectra were divided into three spectral regions 700-400, 1700-800, and 3700-2800 cm(-1). The soil was found rich in organic matter and capable of retaining metals as abundant peaks were observed in the mid-infrared region. The mineralogical analysis of soil samples testified silicon oxides and zeolite as major mineral phases. The XPS spectra showed broad peaks of As(III), As2O3, As4S4, PbO2, and PbCo3. The study concludes that the source identification of metal(oid)s in the upper Indus is crucial to find out the particular source of contamination in the soil.