Data refer to 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 (i.e., CB at 21°N 20°W; M1U at 12°N 23°W; M2U at 14°N 37°W; M4U at 12°N 49°W; Guerreiro et al., 2017) 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. Auxiliary environmental data regarding the mixed layer depth (MLD) are provided for the sampling period at all four trap sites, while Sea Surface Temperature (SST), wind velocity, daily precipitation and sea surface Chl-a concentrations are only provided for sites M1 and CB. All data in supplement to Guerreiro et al. (2019), with links to Guerreiro et al. (2017) and Korte et al. (2017, 2020) (see https://doi.pangaea.de/10.1594/PANGAEA.881457).