This dataset provides absolute abundance data of planktonic foraminifera (identified at the species level), benthic foraminifera and radiolaria (both counted as total numbers). The microfossils were obtained from a sediment core collected at 4394 m water depth off the Cabo Verde archipelago which covers most of the Holocene Epoch. Counts were performed on the >150 µm sediment fraction, with a minimum of 300 planktonic foraminifera specimens per sample.