Natural minerals play a vital role and exhibit unique electronic and structural properties that can be attributed to the presence of gold. Therefore, research on the chemical bonding of these materials is essential for contributing to better exploration, separation, and recovery techniques. The study of minerals from mining areas and their differences in correlation to Au contributes to an understanding of the chemical forms of invisible gold in rocks as well as their association with other mineral deposits. Here, we investigate the structural chemistry of gold (Au) and pathfinder elements in soil sediments (Au concentrates) containing host minerals of pyrite (FeS2), magnetite (Fe3O4), and quartz (SiO2) identified by X-ray diffraction (XRD). The samples were collected at an alluvial small-scale mining site and investigated by X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) at the Au 2p3/2 and Ag 1s absorption edges. XANES shows that the average valence states of Au have different weights of Au0, Au1+ and Au3+ depending on the composition of the host minerals at the mineral deposit. EXAFS shows that the interatomic Au-Au distances increase to 2.99–3.03 Å compared to 2.85 Å for Au metal, while the Ag-Ag distances increase to 2.93–2.97 Å compared to Ag metal of 2.86 Å. As shown in this work, XANES and EXAFS reveal the structural composition and chemical bonding of Au and Ag in host minerals that play an important role in the formation and stability of Au-associated mineral deposits. The results also reveal the alloying of Au with Ag and its association with S and O ligands in the host minerals as indistinguishable in X-ray diffraction. The knowledge will aid in mineral exploration and extraction based on geochemical data of the constituent minerals in potential geological zones.