Underlying bedrock is often the source of elevated levels of potentially toxic elements (PTEs) (including Ni and Cr) in soils, which can be at concentrations exceeding regulatory guidelines for the protection of human health. However geogenic contaminants are often not significantly bioavailable to humans as they are bound tightly within the soil matrix. Therefore oral bioaccessibility testing can be used to refine human health risk assessment by quantifying bioaccessible PTEs in soils, but should be augmented with soil mineralogy data to support its use in risk assessment. Elemental mapping using Electro Probe Microanalysis (EPMA) and mineralogical mapping using QEMSCAN®, an automated mineral/phase analysis system based on a scanning electron microscope, were combined with quantitative X-ray Diffraction (XRD) and previous oral bioaccessibility and non-specific sequential extraction (CISED) results for 3 soil samples overlying Palaeogene basalt lavas in Northern Ireland, to determine the effect of soil mineralogy on oral bioaccessibility of Ni and Cr. Results indicate that Cr concentrations are principally related to recalcitrant chrome spinel and primary iron oxides, which explains the relatively low bioaccessibility of Cr. In contrast, Ni is more widely dispersed within the soils, with a proportion of total Ni found in carbonates and weathering products, including secondary iron oxides and precursor clay minerals, leading to the higher oral bioaccessibility measurements recorded for Ni than Cr.