We compiled modern and fossil relative abundance of coccolithophore species Florisphaera profunda from published and unpublished datasets, along with ocean environmental variable data from satellite remote sensing and physical measurements. The database includes relative abundances of F. profunda in sediment trap (n = 26) and core-top (n = 1258), and sediment core samples (n = 104). Downcore data covers the Last Glacial Maximum (n = 94, 24-19 ka) or the Mid-to-Late Holocene (n = 77, <6 ka). This database allows studying modern and past biogeography of F. profunda as a response to changing ocean and climate conditions, “Quantitative reconstruction of primary productivity in low latitudes during the last glacial maximum and the mid-to-late Holocene from a global Florisphaera. profunda calibration dataset” (Hernández-Almeida et al., 2018).