The surface structure and hydrophilicity of synthetic nanocrystalline apatite with strongly bound citrates on their surface are here investigated at the molecular level, by combining advanced IR spectroscopy, microgravimetry and adsorption microcalorimetry. Citrate are found to form unidentate-like and ionic-like complexes with surface Ca²⁺ ions, with a surface coverage closely resembling that present in bone apatite platelets (i.e., 1 molecule/(n nm)², with n ranging between 1.4 and 1.6). These surface complexes are part of a hydrated non-apatitic surface layer with a sub-nanometre thickness. Noticeably, it is found that the hydrophilicity of the nanoparticles, measured in terms of adsorption of water molecules in the form of multilayers, decreases in a significant extent in relation to the presence of citrates, most likely because of the exposure toward the exterior of –CH₂ groups. Our findings provide new insights on the surface properties of bio-inspired nano-apatites, which can be of great relevance for better understanding the role of citrate in determining important interfacial properties, such as hydrophobicity, of bone apatite platelets. The evaluation and comprehension of surface composition and structure is also of paramount interest to strictly control the functions of synthetic biomaterials, since their surface chemistry strongly affects the hosting tissue response.