Tropical oceans provide a benchmark for future primary productivity in increasingly warmer, stratified and nutrient-depleted waters. In this context, we assess the export fluxes of calcifying phytoplankton (coccolithophores) across the tropical North Atlantic, from upwelling affected NW Africa, via three ocean sites along 12°N to the Caribbean. Sampling was undertaken by means of a spatial array of four time-series sediment traps collecting particle fluxes in two-week intervals, from October 2012 to February 2014, allowing to track temporal changes along the southern margin of the North Atlantic central gyre. Species composition and seasonal export fluxes of coccolithophores show steep gradients in two groups. Upper photic zone (UPZ) and placolith-bearing species dominated by Emiliania huxleyi and Gephyrocapsa oceanica are most abundant in the mesotrophic surface waters of the Cape Blanc upwelling system off NW Africa. They decline gradually towards the Caribbean, paralleled by increasing surface temperatures and decreasing surface chlorophyll-a. Meanwhile the abundance of lower photic zone (LPZ) species Florisphaera profunda and Gladiolithus flabellatus increase in the same direction, reaching fluxes up to 3–5 times higher in the western end of the transect compared to the UPZ flora in mesotrophic waters. Adapted to low light conditions, the LPZ species follow the geostrophic wind-forced deepening of the thermocline/nutricline westward in ever lower species diversity towards the Caribbean. Temporal changes were marked by weak seasonality in coccolith fluxes at all four sites, modulated by latitudinal migration of the Intertropical Convergence Zone (ITCZ) at the tropical sites M1, M2 and M4, and by spatiotemporal variation in wind-forced upwelling at site CB. A seasonal mismatch was observed between LPZ and UPZ-oligotrophic taxa (i.e. Umbellosphaera spp., Rhabdosphaera spp.) vs. UPZ-opportunistic species (E. huxleyi, G. oceanica) at the western site M4 contrasting with the more similar seasonal patterns amongst all species towards site CB. We interpret this as reflecting the entire photic zone becoming increasingly nutrient enriched towards east whenever wind-forced mixing occurs due to the eastward shoaling of the thermocline/nutricline. Our synoptic observations of seasonally resolved export fluxes at four sites contribute to the spatiotemporal understanding of coccolithophore fluxes across the entire tropical North Atlantic, urging for considering phytoplankton- and carbonate production across the entire photic zone when projecting the effects of ocean warming on future primary production.