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 bulk organic matter stable isotopes (δ13C and δ15N) from a sediment record collected in front of Faro (POPEI-VC2B), along the Algarve coast, obtained with a vibro-core sampler during the POPEI Cruise in 2008. Bulk organic carbon isotope analysis was coordinated by Dr Aldo Shemesh (Weizmann Institute) and performed at the Cornell University Stable Isotope Laboratory via Elemental Analysis coupled to Isotope Ratio Mass Spectrometry (EA-IRMS), Carlo Erba NC2500 / Thermo Scientific Delta V Advantage system.