The data were generated at ESRF beamline ID22 with an incident energy at 17 keV. Coccoliths were analyzed with 0.1 µm x 0.1 µm pixel size and 2 s time analysis per pixel. All coccoliths were picked from samples from Murtinheira section at Cabo Mondego, Portugal dated to the lower Bajocian (Middle Jurassic). The sample positions in the section are described in Suchéras-Marx et al. (2012). Discorhabdus striatus_1 from sample CM9 ; _Watznaueria britannica_1-_W. britannica_2 from sample CM17 ; _D. striatus_2 from sample CM26 ; _D. striatus_3-_W. britannica_3-_W. britannica_4-_W. contracta from sample CM35 ; D. striatus_4-_Watznaueria indet.1-Watznaueria indet.2 from sample CM60 ; _W. britannica_5-_W. britannica_6-_W. britannica_7 from sample CM62. 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) may be used for all coccoliths. Those data were acquired through the project EC811 at ESRF. Similar results are published in Suchéras-Marx et al. (2016).