The data were generated at ESRF beamline ID22 with an incident energy at 17 keV. Crepidolithus crassus, Discorhabdus striatus and Watznaueria contracta were analyzed with 0.1 µm x 0.1 µm pixel size and 2 s time analysis per pixel. Coccoliths were picked from sample CM35 from Murtinheira section at Cabo Mondego, Portugal. Sample position in the section in Suchéras-Marx et al. (2012). The sample is dated from the lower Bajocian (Middle Jurassic). Data treatment is made using PyMCA. For each calcareous nannofossil, the raw data (.edf in .zip) and the pondered spectrum (.csv) are given. The fit file given (.cfg) was used for all coccoliths. Those data were acquired through the project EC811 at ESRF. Similar results published in Suchéras-Marx et al. (2016).