The data were generated at ESRF beamline ID21 with an incident energy at 7.5 keV. Coccolithus pelagicus, Discorhabdus striatus, Helicosphaera carteri and Watznaueria britannica were analyzed with 0.4 µm x 0.4 µm pixel size and 3 s time analysis per pixel. Calcidiscus leptoporus was analyzed with 0.2 µm x 0.2 µm pixel size and 1.5 s time analysis per pixel. Dicoaster falcatus 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 in .zip) 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. Coccolithus pelagicus is from North Atlantic sediment coretop GIK23066. Discorhabdus striatus is from Murtinheira section at Cabo Mondego, Portugal sample CM9. Watznaueria britannica is from Murtinheira section at Cabo Mondego, Portugal sample CM60. Sample position in the Murtinheira section at Cabo Mondego in Suchéras-Marx et al. (2012). Helicosphaera carteri and Calcidiscus leptoporus are from South Atlantic sediment coretop GeoB3721-4. Discoaster falcatus is from Wilson lake core, NJ, USA.