Seven different labs XRF scanned the same seven marine sediment sections. Additionally, four labs XRF scanned pellets that had known compositions determined by ICP-ES and ICP-MS. These datasets contain the XRF scanning results of the seven sediment section and four pellets.The seven 1.5 m core sections of marine sediment core used in this study were drilled during Integrated Ocean Drilling Program (IODP) Expedition 346 at Site U1424 in the Japan Basin (40°11.39'N, 138°13.90'E, 2808 m water depth) and Site U1425 on the Yamato Rise (39°29.43' N, 134°26.55' E, 1909 m water depth). The sections selected (Hole U1424C Sections 1H4, 2H5, 3H5 and Hole U1425C Sections 2H3, 2H4, and 2H6, and 3H6) cover a range of sediment compositions. U-channels extracted continuous marine sediment approximately 1 cm thick from the center of each split core section. One lab scanned sections from different holes at the same sites (U1424A, U1425B, and U1425D) that were stratigraphically aligned with the sections listed above.Over the course of four years (2014 to 2017), the set of seven u-channels was shipped around the world to seven labs with XRF scanners including, in no particular order, the Kochi Core Center at Kochi University (Japan), IODP Core Repository at Texas A&M University (U.S.A.), Nanjing Normal University (China), Rosenstiel School of Marine and Atmospheric Science at the University of Miami (U.S.A.), ETH Zurich (Switzerland), Woods Hole Oceanographic Institution (U.S.A.), and the Royal Netherlands Institute of Sea Research (The Netherlands). We intentionally do not identify which lab generated which scans, as many of the variables (e.g., X-ray tube aging, detector aging, and/or dehydration of the core material) could affect any instrument at various times or be exacerbated during the transit between labs. Instead, we label the XRF scans #1-#7 in the order in which they were scanned.The lead investigators overseeing the XRF scanning in these labs were shipboard participants on IODP Expedition 346 and are among the authors of this paper. The only instructions to each lab were "to XRF scan the seven sediment sections at 1mm or 2mm resolution using the approach and elements typical for paleoceanographic research performed in your lab." To emulate variations in the XRF results that have been previously published, these simple guidelines were intentionally broad and general to determine the degree of intercomparability between the labs amongst all the different settings and nuances of XRF scanning.The labs used various types and different generations of XRF scanning instruments (4 Avaatech Core Scanners, 2 ITRAX Core Scanners, and 1 Geotek Core Scanning Logger) with different X-ray sources (Rhodium, Molybdenum). Three of the labs scanned the cores at two or three excitation energies (e.g., 10 kV, 30 kV, and 50 kV). Each lab reported a different suite of elements, but all included Ca, Fe, K, Mn, Si, Sr, Ti, and Zr. Six labs also reported Al, Br, Cr, Cu, Ni, Pb, Rb, S, and Zn and five labs reported and Ba, Cl, Ga, Mo, V, and Y.In addition to the seven core sediment sections, we freeze-dried and powdered four discrete samples that were pressed into disc-shaped pellets about 2 cm in diameter from nearby Core MD01-2407 on the Oki Ridge (37°04'N, 134°42'E, 932m water depth). The four samples have a similar matrix to the seven sediment sections scanned in this study. The four samples from Core MD01-2407 covered a range of sediment types (calcareous, siliceous, light-, and dark-colored; Kido et al., 2007) that span the dynamic range of at least Fe and Ca element cps scanned for this study. A set of four pellets was sent to four of the seven labs (1 ITRAX and 3 Avaatech) involved in the study to be scanned using the same instrument parameters they used on the sediment sections. Three labs used the same instrument and parameters used for the sediment section, but the fourth lab replaced the X-ray tube in between scanning the pellets and sediment sections. The major and trace element concentrations of the pellets were also analyzed by inductively coupled plasma (ICP)-optical emission spectrometry (OES) and ICP-mass spectrometry (MS) in the Analytical Geochemistry Facilities at Boston University, Boston, MA, USA. The ICP analyses had ~2% precision and a standard reference material analyzed as an unknown alongside the samples was accurate within precision.