This study focuses on Pleistocene–Holocene sediments from the Shatsky Rise (Ocean Drilling Program Site 1209B, NW Pacific Ocean). We quantify the contribution of calcite made by coccoliths in oceanic sediments, investigating the role of calcareous nannoplankton during the last 450 ka. Coccolith carbonate constitutes 60–90% of bulk carbonate. Coccolith carbonate accumulation rates (CARs) and CaCO3 fine fraction confirm that coccolithophores are major contributors to the carbonate export and accumulation. Primary productivity shows highest values from marine isotope stage (MIS) 12 to 8. Thereafter, although coccolith calcite content remains high, other sediment components, such as as foraminifera and biogenic opal, seem to be favored, perhaps related to an increase in fertilization by eolian dust. Our results demonstrate the important role of coccolithophore production and sedimentation on the regulation of ocean carbonate chemistry on time scales >1000–100 000 years. On glacial–interglacial scales, coccolithophore productivity could have affected deep-water saturation by buffering deep-sea CO2 through increased carbonate dissolution episodes. Spectral and wavelet analyses are consistent with CARs primarily driven by glacial–interglacial variability and obliquity-controlled changes. Coccolith-based paleoceanographic reconstructions allow us to establish that during the last 450 ka the mid-latitudes of the NW Pacific are controlled by the dynamics of the El Niño Southern Oscillation perturbations and Boreal Monsoon system.