A combined approach based on multiple X-ray analytical techniques and conventional methods was adopted to investigate the distribution and speciation of Cr in a polluted agricultural soil, from the bulk-scale down to the (sub)micro-level. Soil samples were collected from two different points, together with a control sample taken from a nearby unpolluted site. The bulk characterization revealed that the polluted soils contained much higher concentrations of organic matter (OM) and potentially toxic elements (PTE) than the control. Chromium was the most abundant PTE (up to 5160 g kg−1), and was present only as Cr(III), as its oxidation to Cr(VI) was hindered by the high OM content. According to sequential extractions, Cr was mainly associated to the soil oxidisable fraction (74%) and to the residual fraction (25%). The amount of Cr potentially bioavailable for plant uptake (DTPA-extractable) was negligible. Characterization of soil thin sections by micro X-ray fluorescence (μXRF) and field emission scanning electron microscopy coupled with microanalysis (FEGSEM-EDX) showed that Cr was mainly distributed in aggregates ranging from tens micrometres to few millimetres in size. These aggregates were coated with an aluminosilicate layer and contained, in the inner part, Cr, Ca, Zn, P, S and Fe. Hyperspectral elaboration of μXRF data revealed that polluted soils were characterised by an exogenous organic-rich fraction containing Cr (not present in the control), and an endogenous aluminosilicate fraction (present also in the control), coating the Cr-containing aggregates. Analyses by high-resolution micro X-ray computed tomography (μCT) revealed a different morphology of the soil aggregates in polluted soils compared with the control. The finding of microscopic leather residues, combined with the results of bulk- and micro-characterizations, suggested that Cr pollution was likely ascribable to soil amendment with tannery waste-derived matrices. However, over the years, a natural process of Cr stabilization occurred in the soil thus reducing the environmental risks.