Fluorapatite (FAp, nominally Ca5(PO4)3F) is the most common phosphate mineral at the Earth’s surface and a main host for rare earth elements (REE) in magmatic and hydrothermal ore deposits and in marine sediments. Our understanding of the enrichment process of REE in FAp rests upon two foundations: (1) being able to elucidate the thermodynamic driving force for their partitioning between the Ca1 and Ca2 structural sites, and (2) being able to determine how the substitution of REE(III) for Ca(II) is charge compensated. A main unsolved question is the marked preference of the larger light REE (lanthanum → samarium) for the smaller Ca2 site. We used density functional theory (DFT) and high-energy resolution fluorescence-detected extended X-ray absorption fine structure (HERFD-EXAFS) spectroscopy to gain detailed insight into the bonding energy, electronic structure, and short-range order of cerium (Ce) in natural FAp. Results show that Ce(III) has a marked preference for a Ca2 site where the nearest five-valent phosphorous cation is replaced with a tetravalent silicon cation, thus balancing the charge excess of the Ce impurity locally. Atomic charge calculations show that the Ca2 site is more ionic than the Ca1 site and that the energetics of the site preference is linearly correlated to the ionization energy of the substituent. Cations with a low energy of ionization, like Ce, preferably occupy the Ca2 site. Novel combination of HERFD-EXAFS spectroscopy and DFT appears to be the most straightforward and reliable way to assess the crystal chemistry of trace elements in compositionally complex natural materials, and opens a previously unavailable avenue for mechanistic investigation of metal enrichment in ore deposits.