Optical microscopy, confocal Raman micro-spectrometry, X-ray photoelectron micro-spectroscopy (XPS) and synchrotron based micro-X-ray fluorescence (XRF), micro-X-ray absorption near edge spectroscopy (XANES) and micro-extended X-ray absorption fine structure (EXAFS) were used to investigate the reduction of aqueous Cr(VI) by pyrite. Special emphasis was placed on the characterisation of the solid phase formed during the reaction process. Cr(III) and Fe(III) species were identified by XPS analyses in addition to non-oxidised pyrite. Optical microscopy images and the corresponding Raman spectra reveal a strong heterogeneity of the samples with three different types of zones. (i) Reflective areas with Eg and Ag Raman wavenumbers relative to non-oxidised pyrite are the most frequently observed. (ii) Orange areas that display a drift of the Eg and Ag pyrite vibration modes of −3 and −6 cm−1, respectively. Such areas are only observed in the presence of Cr(VI) but are not specifically due to this oxidant. (iii) Bluish areas with vibration modes relative to a corundum-like structure that can be assigned to a solid solution Fe2−xCrxO3, x varying between 0.2 and 1.5. The heterogeneity in the spatial distribution of chromium observed by optical microscopy and associated Raman microspectroscopy is confirmed by μ-XRF. In agreement with both solution and XPS analyses, these spectroscopies clearly confirm that chromium is in the trivalent state. XANES spectra in the iron K-edge pre-edge region obtained in rich chromium areas reveal the presence of ferric ion thus revealing a systematic association between Cr(III) and Fe(III). In agreement with Raman analyses, Cr K-edge EXAFS can be interpreted as corresponding to Cr atoms involved in a substituted-type hematite structure Fe2−xCrxO3.