The North African desert margin is considered one of the areas most sensitive to future climate changes. Improved knowledge about Holocene climatic variability and environmental responses on millennial to centennial scale will help to refine scenarios related to future climate changes. This data set presents calibrated XRF core scanning data (Ca, Sr, Fe, Mn, S, K, Ti) of a ~20 m long Holocene lake sediment sequence from Lake Sidi Ali located in the Middle Atlas, Morocco. The ITRAX core scanner measurements were obtained every 1 mm and calibrated with depth equal quantitative Spectro Xepos XRF data (see. Schmidt et al. 2023, doi:10.1594/PANGAEA.960365) using the multivariate log-ratio calibration model of Weltje et al. 2015 (doi:10.1007/978-94-017-9849-5_21). According to the 210Pb and pollen-based 14C chronology, the calibrated XRF scanning data have a c. annual temporal resolution.