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 different nutrient sources and paleoceanographic features of the Iberian Margin and to reconstruct primary productivity and phytoplankton community variability over the past 1,000 years.This dataset presents biogenic silica (BSi) content from a sediment record collected west of the Tagus River mouth (POS-26B and -26G), in the central region of the Portuguese continental shelf, using box-core and gravity coring systems during the Poseidon cruise POS287 in 2002. Biogenic silica was measured at the Geological Survey of Denmark and Greenland using the weak base (Na2CO3) extraction method (DeMaster, 1991) and determined by spectrophotometry (blue ammonium-molybdate method, Mullin and Riley, 1955). Biogenic silica concentrations were calculated and corrected for mineral dissolution using the intercept of a linear regression, with the basic assumption that mineral-derived silica dissolves at a constant rate throughout the extraction whereas the biogenic silica dissolves within the first two hours (Barão et al., 2015).