The Ipubi and Romualdo Formations are Cretaceous units of the Araripe Basin (Santana Group). The first and most ancient was deposited in a lake environment, and some fossils were preserved in shales deposited under blackish conditions. The second was deposited in a marine environment, preserving a rich paleontological content in calcareous concretions. Considering that these two environments preserved their fossils under different processes, in this work we investigated the chemical composition of two fossilized specimens, one from each of the studied stratigraphic units, and compared them using vibrational spectroscopy techniques (Raman and IR), X-ray diffraction and large-field energy-dispersive X-ray spectroscopy (EDS) mappings. Calcite was observed as the dominant phase and carbon was observed in the fossils as a byproduct of the decomposition. The preservation of hydroxide calcium phosphate (Ca10(PO4)6(OH)2, hydroxyapatite) was observed in both fossils. In addition, it was observed that there was a smaller amount of pyrite (pyritization) in the Romualdo Formation sample than in the Ipubi one. Large-field EDS measurements showed the major presence of the chemical elements calcium, oxygen, iron, aluminum and fluoride in the Ipubi fossil, indicating a greater influence of inorganic processes in its fossilization. Our results also suggest that the Romualdo Formation fossilization process involved the substitution of the hydroxyl group by fluorine, providing durability to the fossils.