To develop a solid scientific basis for maintaining soil quality and formulating effective remediation strategies, it is critical to determine how environmentally-important trace metals are sequestered in soils at the molecular scale. The speciation of Mn, Fe and Cu in soil organic matter has been determined by synchrotron-based techniques: extended X-ray absorption fine structure (EXAFS) and X-ray absorption near edge structure (XANES). We show the structural similarity between the surface complexes of Mn(II), Fe(III) and Cu(II). These cations are bound to the surface through oxygen atoms. Each one presents a more or less tetragonal-distorted octahedral geometry. The use of X-ray absorption spectroscopy provides a relevant method for determining trace-metal speciation in both natural and contaminated environmental materials.