Bio-inspired apatite nanoparticles precipitated in the presence of citrate ions at increasing maturation times are characterized in terms of structure, size, morphology, and composition through advanced X-ray total scattering techniques. The origin of the platy crystal morphology, breaking the hexagonal symmetry, and the role of citrate ions is explored. By cross-coupling the size and shape information of crystal domains with those obtained by atomic force microscopy on multidomain nanoparticles, a plausible mechanism underlying the amorphous-to-crystal transformation is reconstructed. In the present study, citrate plays the distinct roles of inducing the platy morphology of the amorphous precursor and controlling the thickness of the Ca-deficient apatite nanocrystals. These findings can open new scenarios also in bone mineralization, where citrate might have a broader role to play than has been thought to date.