Carbonated apatites represent an important class of compounds encountered in many fields including anthropology, archeology, geology, medicine and biomaterials engineering. They constitute, in particular, the mineral part of bones and teeth, are found in sedimentary settings, and are used as biomimetic compounds for the development of bone tissue engineering scaffolds. Whether for assessing the degree of biomimetism of synthetic apatites or for better understanding diagenetic events, their thorough physico-chemical characterization is essential, and includes, in particular, the evaluation of their carbonate content. FTIR is especially well-suited for such a goal, as this spectroscopy technique requires only a low amount of specimen to analyze, and carbonate ions exhibit a clear vibrational signature. In this contribution, we critically discuss several FTIR-approaches that may be (or have been) considered in view of carbonation quantification. The best methodology appears to be based on the analysis of the ν3(CO3) and ν1ν3(PO4) modes. The area ratio rc/p between these two contributions was found to be directly correlated to the carbonate content of the samples (R² = 0.985), with the relation wt.% CO3 = 28.62 * rc/p + 0.0843. The method was validated thanks to titrations by coulometry assays for various synthetic reference samples exhibiting carbonate contents between 3 and 7 wt.%. The FTIR carbonate quantification methodology that we propose here was also tested with success on three skeletal specimens (two bones/one tooth), after elimination of the collagen contribution. Comparative data analysis is also presented, showing that the use of other vibration bands, or only peak heights (instead of peak areas), leads to significantly lower correlation agreement. This FTIR data treatment methodology is recommended so as to limit errors on the evaluation of carbonate contents in apatite substrates.