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 (EBUS) 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 lipid biomarkers (including n-C20 to n-C35 n-alkenes, C16 to C32 n-alcohols, C27 to C30 sterols, C37 to C38 alkenones, phytol, bisnorhopane, and C30 and C32-1,15 diols) from a sediment record collected off the mouth of the Douro River (POS287-06G), in the north-western region of the Portuguese continental shelf, using a gravity coring system during the Poseidon cruise POS287 in 2002. Lipid biomarker analysis were conducted at the EMSO-Gold Biogeochemistry Lab at IPMA using gas chromatography coupled with flame ionization detection (GC-FID), Scion, mod. 436; and mass spectrometry (GC-MS), Bruker Scion, 456-GC/SQ system.