This dataset contains quantitative records of calcareous nannofossil assemblages and coccolith accumulation rates from sediment cores collected along the western Iberian Margin (Porto, Lisbon, and Faro sites). The data cover the Common Era (~0–2000 years BP) and were produced to document high-resolution variations in primary productivity and surface ocean conditions under the influence of the Iberian upwelling system. Sediment cores were retrieved from the inner shelf at water depths of 80–96 m during the PALEO1 (R/V Poseidon, 2002) and POPEI0108 (NRP Auriga, 2008) oceanographic campaigns. In total, 166 sediment samples were analysed (71 from Porto, 37 from Lisbon, and 41 from Faro). Sample preparation followed the random settling technique of Flores and Sierro (1997), ensuring homogeneous coccolith distribution on slides. Calcareous nannofossils were identified and quantified under polarized-light microscopy at 1250× magnification. Absolute abundances (coccoliths/g) were calculated following Flores and Sierro (1997), and coccolith accumulation rates (NAR) were derived by combining coccolith concentration, dry bulk density, and sedimentation rates from published age models. The dataset includes absolute and relative abundances of coccolithophore taxa, total coccolith concentrations and NAR values. These data provide the basis for reconstructing primary productivity patterns and environmental variability along the western Iberian Margin during key climatic intervals of the Common Era, including the Medieval Climate Anomaly, Little Ice Age, and Industrial Era.