Extracted bioapatite (BAp) from archaeological skeletal remains is used in studies reconstructing diet, mobility, and lifestyle of past human populations. Despite this, few investigations have researched extracted BAp, although some of them suggest that chemical extraction may alter BAp structure and composition. Here, we apply attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy on BAp extracted from archaeological bones: 29 human individuals of two medieval-postmedieval necropolises and 30 non-humans from Roman and medieval times, all from northwestern Spain. Statistical treatment includes principal component analysis (PCA) on (i) selected peaks (dPCA) and (ii) whole spectrum (tPCA). Extracted BAp shows the characteristic vibrations of the main components of a non-stoichiometric apatite, as well as other minor vibrations related to labile components. PCA results are also consistent in revealing the structural and compositional features of BAp, although tPCA results correlate better to BAp IR indices and properties than dPCA results. Significant differences in BAp spectral signal were found between human and non-human bone, collections (i.e., necropolises), human groups (non-adults vs. adults), human bone type (long bones vs. ribs), and non-human groups (bovine vs. ovicaprid). Thus, extracted BAp also retains crucial information that could be related to pre- and postmortem modifications of bone.