Coccolithophores contribute significantly to the marine primary productivity and play a unique role in ocean biogeochemistry by using carbon for photosynthesis (biological pump) and also for calcification (carbonate pump). Despite the importance of including coccolithophores in global climate models to allow better predictions of the climate system's responses to planetary change, highly uncertain coccolithophore paleoproductivity past reconstructions mostly relied on proxies dependent on accumulation and sedimentation rates, and preservation conditions. In this study we used an independent proxy, based on the coccolith fraction (CF) Sr/Ca ratio, to reconstruct coccolithophore productivity. We used the marine sediment core MD03-2699 from the western Iberian margin (IbM), spanning the glacial/interglacial cycles of Marine Isotope Stage (MIS) 12 to MIS 9. We found that IbM coccolithophore productivity was controlled by changes in the oceanographic conditions, such as in SST, the competition for nutrients with other phytoplankton groups and insolation. Long-term coccolithophore productivity was primarily affected by variations in the dominant water mass. Polar and subpolar surface waters during glacial substages were associated with decreased coccolithophore productivity, with strongest productivity minima being concomitant with Heinrich-type events (HtE). Subtropical, nutrient-poorer waters during interglacial substages, i.e. MIS 11c, might have lead to intensified competition for nutrients with diatoms resulting in intermediate levels of coccolithophore productivity. The transition from interglacial to glacial substages was likely associated with increasing presence of nutrient-richer waters, possibly with lower silica content than riverine discharges and mostly fed by either upwelling or surface waters of northern origin. This minimized the competition with diatoms and coccolithophores reached their productivity maxima. Climatic conditions during colder periods forced coccolithophores to change their phenology contributing to the dissonance between the CF Sr/Ca derived coccolithophore productivity and nannofossil accumulation rate and total alkenone flux, which is interpreted as a consequence of the narrowing yearly time-window for coccolithophore productivity.