The Iberian Margin, located in the mid-latitude North Atlantic at the western edge of the European continent, is a key region for climate and oceanographic research. The Portuguese western coast marks the northernmost boundary of the Canary Current upwelling system, experiencing seasonal wind-driven coastal upwelling from May to September. Eastern Boundary Upwelling Systems are among the most productive regions in the global ocean. They play a vital role in climate regulation and support both local and global fisheries. As part of the ICW3P project (PTDC/CTA-CLI/2884/2021) 'Impact of climate warming in the coastal upwelling system and primary production off Portugal: a study linking classical and emerging proxies', this study presents multi-proxy records from three inner-shelf sediment sequences. The project aimed to evaluate the sources of organic matter in the Iberian Margin and to reconstruct primary productivity and phytoplankton community variability over the past 1,000 years. This dataset presents the X-ray fluorescence records from a sediment record collected off the Douro River mouth (PO287-06-2G), inner-shelf of the northwestern Portugal, obtained with a gravity corer sampler during the Poseidon Cruise PO287 in 2002. X-ray fluorescence analysis was conducted to examine variations in sediment elemental composition, providing insights into terrigenous or biological inputs and environmental changes. Analyses were performed at the EMSO-GOLD Laboratory at the Portuguese Institute of the Sea and Atmosphere (DivGM-IPMA) using a 4th generation Avaatech XRF core scanner. Scanning was done with 10, 30, and 50 kV, with 200, 250, and 1000 μA, respectively. Parameters such as Throughput (regulating signal flow to prevent detector overload) and Area Count (intensity measurement at each analysis point) were optimized to enhance accuracy and efficiency. Detected data were normalized over throughput corrections to account for signal flow variability, ensuring consistent element quantification. Real-time (total acquisition time) and Live Time (effective detection time) were differentiated, and Acquisition Time at each position was adjusted to maximize the signal-to-noise ratio. Data was processed using BRIGHTSPEC bAxil software.