The data were generated at ESRF beamline ID21 with an incident energy at 7.5 keV. Cribrosphaerella ehrenbergii, Calcidiscus leptoporus, Gephyrocapsa oceanica, Helicosphaera carteri and Watznaueria barnesae were analyzed with 0.4 µm x 0.4 µm pixel size and 3 s time analysis per pixel. Marthasterites spineus was analyzed with 0.5 µm x 0.5 µm pixel size and 3 s time analysis per pixel. Data treatment is made using PyMCA. For each calcareous nannofossil, the raw data (.edf) and the pondered spectrum (.csv) are given. One fit file is given (.cfg). It may be applied to any sample but for further calculation, new fit file specifically adapted to the sample should be used. Those data were acquired through the project ES113 at ESRF.Cribrosphaerella ehrenbergii is from Niobrara chalk, USA (unknown coordinates). Watznaueria barnesae is from Chaabet el Attaris section, Tunisia (sample CG407; unknown coordinates). Marthasterites spineus is from sample DG4.50 from unknown provenance. Calcidiscus leptoporus is from South Atlantic sediment coretop GeoB3721-4. Gephyrocapsa oceanica and Helicosphaera carteri are from western equatorial Pacific sediment core MD05-2920.