This dataset provides absolute abundance data of planktonic foraminifera (identified at the species level) and 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. Combined stable isotopes (δ13C and δ18O) and Mg/Ca ratios are included for the surface-dwelling planktonic foraminifera Globigerinoides ruber albus (G. ruber sensu stricto morphotype following Wang, 2000) and the sub-thermocline dwelling Globorotalia truncatulinoides from the 315-400 μm sediment fraction. Al/Ca, Fe/Ca and Mn/Ca measurements to monitor potential test contamination are also provided. Additionally, this dataset contains δ13C and δ18O for the epibenthic foraminifera Cibicidoides wuellerstorfi.