A gem-grade apatite from Brazil of general composition (Ca,Na)10[(P,Si,S)O4]6(F,Cl,OH)2 has been studied using single-crystal X-ray and neutron diffraction together with synchrotron powder X-ray diffraction. Earlier electron microscopy studies had shown the nominally single-phase apatite contains an abundant fluorapatite (F-Ap) host, together with chloro-hydroxylapatites (Cl/OH-Ap) guest phases that encapsulate hydroxylellestadite (OH-El) nanocrystals. While the latter features appear as small (200–400 nm) chemically distinct regions by transmission electron microscopy, and can be identified as separate phases by synchrotron powder X-ray diffraction, these could not be detected by single-crystal X-ray and neutron analysis. The observations using neutron, X-ray and electron probes are however consistent and complementary. After refinement in the space group P63/m the tunnel anions F− are fixed at z = ¼ along <001>, while the anions Cl− and OH− are disordered, with the suggestion that O-H···O-H··· hydrogen-bonded chains form in localized regions, such that no net poling results. The major cations are located in the 4f AFO6 metaprism (Ca+Na), 6h ATO6X tunnel site (Ca only), and 6h BO4 tetrahedron (P+Si+S). The structural intricacy of this gem stone provides further evidence that apatite microstructures display a nano-phase separation that is generally unrecognized, with the implication that such complexity may impact upon the functionality of technological analogues.