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International Ocean Discovery Program Expedition 401 recovered 983 m of sediment from Portugal’s southwest margin in the northeast Atlantic Ocean at Site U1609 (37°22.6259′ N, 9°35.9120′ W; 1659.5 m water depth). This site was designed to recover the distal contourites deposited by the Mediterranean Overflow Water contour current from the late Miocene to the Pleistocene. We report semiquantitative elemental results from X-ray fluorescence scanning of sediment cores from Site U1609 (Holes U1609A and U1609B) scanned at a 4–5 cm resolution from ~202 to 509 m core depth below seafloor, Method A, equivalent to ~4.52 to ~7.8 Ma. Raw element intensities (in counts per second) for Al, Si, Ca, Ti, Mn, Fe, Rb, Sr, Zr, and Ba are presented here and correlated with lithofacies variations. We also identify biogenic-terrestrial input proportions and illustrate downcore cyclicity and correlation patterns between terrigenous components (Al, Si, Ti, Mn, and Ba), as well as their anticorrelations with biogenic (Ca and Sr) inputs. The cyclical variations in elemental ratios may help stratigraphic correlation between Holes U1609A and U1609B, astronomical tuning of the spliced record, and sedimentary interpretations of changes to the Mediterranean–Atlantic gateway and the bottom current circulation along the Atlantic margin of Portugal before, during, and after the Messinian Salinity Crisis.