Determining how environmentally important trace metals are sequestered in soils at the molecular scale is critical to developing a solid scientific basis for maintaining soil quality and formulating effective remediation strategies. The speciation of Zn and Ni in ferromanganese nodules from loess soils of the Mississippi Basin was determined by a synergistic use of three noninvasive synchrotron-based techniques: X-ray microfluorescence (microXRF), X-ray microdiffraction (microXRD), and extended X-ray absorption fine structure spectroscopy (EXAFS). We show that Ni is distributed between goethite (alpha-FeOOH) and the manganese oxide lithiophorite, whereas Zn is bound to goethite, lithiophorite, phyllosilicates, and the manganese oxide birnessite. The selective association of Ni with only iron and manganese oxides is an explanation for its higher partitioning in nodules over the soil clay matrix reported from soils worldwide. This could also explain the observed enrichment of Ni in oceanic manganese nodules. The combination of these three techniques provides a new method for determining trace metal speciation in both natural and contaminated environmental materials.