X-ray fluorescence (XRF) core scanners are commonly used for fine-scale geochemical analysis in sediment studies, but data are semi-quantitative and require calibration to convert geochemical element counts to concentrations. Application of XRF core scanning in soil science remains largely untapped. This study employed an ITRAX core scanner to scan grassland soil cores and developed a novel calibration method based on a chemometric approach to characterise soil geochemistry. As soil samples are collected based on depth sampling, this study investigated whether higher resolution element concentrations could be inferred from lower resolution reference samples and if regression models from multiple cores could apply to a new core at the same resolution. Reference concentrations were obtained for all cores at 10 cm intervals, with validation conducted at 1 cm for a single core. Two calibration curve types were proposed: one based on the single core’s 10 cm data to validate references at 1 cm intervals; and another using all cores, with each core serving as a test item after exclusion from the training set. Various preprocessing measures and feature selection techniques were tested. Results showed successful calibration for elements Ca, P, Zn, Sr, and S, with high R2 values of 0.94, 0.93, 0.93, 0.92 and 0.91, respectively. The study presents a novel method for calibrating XRF core scanning element counts, demonstrating its potential for high-resolution soil analysis.