In this work, for the first time, the influence of the coordination environment as well as Ca and P atomic states on biomimetic composites integrated with dental tissue was investigated. Bioinspired dental composites were synthesised based on nanocrystalline calcium carbonate-substituted hydroxyapatite Ca4ICa6IIPO46−xCO3x+yOH2−y (nano-cHAp) obtained from a biogenic source and a set of polar amino acids that modelled the organic matrix. Biomimetic composites, as well as natural dental tissue samples, were investigated using Raman spectromicroscopy and synchrotron X-ray absorption near edge structure (XANES) spectroscopy. Molecular structure and energy structure studies revealed several important features related to the different calcium atomic environments. It was shown that biomimetic composites created in order to reproduce the physicochemical properties of dental tissue provide good imitation of molecular and electron energetic properties, including the carbonate anion CO32− and the atomic Ca/P ratio in nanocrystals. The features of the molecular structure of biomimetic composites are inherited from the nano-cHAp (to a greater extent) and the amino acid cocktail used for their creation, and are caused by the ratio between the mineral and organic components, which is similar to the composition of natural enamel and dentine. In this case, violation of the nano-cHAp stoichiometry, which is the mineral basis of the natural and bioinspired composites, as well as the inclusion of different molecular groups in the nano-cHAp lattice, do not affect the coordination environment of phosphorus atoms. The differences observed in the molecular and electron energetic structures of the natural enamel and dentine and the imitation of their properties by biomimetic materials are caused by rearrangement in the local environment of the calcium atoms in the HAp crystal lattice. The surface of the nano-cHAp crystals in the natural enamel and dentine involved in the formation of bonds with the organic matrix is characterised by the coordination environment of the calcium atom, corresponding to its location in the CaI position—that is, bound through common oxygen atoms with PO4 tetrahedrons. At the same time, on the surface of nano-cHAp crystals in bioinspired dental materials, the calcium atom is characteristically located in the CaII position, bound to the hydroxyl OH group. The features detected in the atomic and molecular coordination environment in nano-cHAp play a fundamental role in recreating a biomimetic dental composite of the natural organomineral interaction in mineralised tissue and will help to find an optimal way to integrate the dental biocomposite with natural tissue.