This dataset (XRF_Benedeni_benedeni_SG-125_126_127_crosslines_cal.csv) contains micro-X-ray fluorescence elemental data of the shell of A. benedeni benedeni specimens SG-125, SG-126, and SG-127. The bivalve shells were collected in 2013 from a shell bed at the top of the Oorderen Member of the Lillo Formation of the Pliocene in Belgium. The collection site was a construction-related temporary outcrop at the Deurganck Dock Lock (now Kieldrecht Lock) in the city of Antwerp, located at 51°16′44″N 4°14′52″E. These measurements were carried out in order to screen for diagenetic alteration, which results in enrichment of certain elements (e.g., Fe and Mn). The specimens were measured in spring 2021 at the Analytical, Environmental, and Geochemistry Research Group (AMGC) of the Vrije Universiteit Brussel, Belgium), on a Bruker M4 Tornado µXRF scanner. This instrument is equipped with a 30 W Rh anode metal-ceramic X-ray tube operated at 50 kV and 600 µA, and polycapillary lens focussing. The measurement was carried out following the methods described in de Winter and Claeys (2017) and Kaskes et al (2021), and consisted of multiple line scans oriented perpendicular to the growth direction. Also provided is an image file (XRF_Benedeni_benedeni_crosslines_locations.png) which shows the location of these line scans on the shell cross sections.