Bone mineral crystallinity is an important factor determining bone quality and strength. The gold standard method to quantify crystallinity is X-ray diffraction (XRD), but vibrational spectroscopic methods present powerful alternatives to evaluate a greater variety of sample types. We describe original approaches by which transmission Fourier transform infrared (FT-IR), attenuated total reflection (ATR) FT-IR, and Raman spectroscopy can be confidently used to quantify bone mineral crystallinity. We analyzed a range of biological and synthetic apatite nanocrystals (10-25 nm) and found strong correlations between different spectral factors and the XRD determination of crystallinity. We highlight striking differences between FT-IR spectra obtained by transmission and ATR. In particular, we show for the first time the absence of the 1030 cm crystalline apatite peak in ATR FT-IR spectra, which excludes its use for analyzing crystallinity using the traditional 1030/1020 cm ratio. The νPO splitting ratio was also not adequate to evaluate crystallinity using ATR FT-IR. However, we established original approaches by which ATR FT-IR can be used to determine apatite crystallinity, such as the 1095/1115 and 960/1115 cm peak ratios in the second derivative spectra. Moreover, we found a simple unified approach that can be applied for all three vibrational spectroscopy modalities: evaluation of the νPO peak position. Our results allow the recommendation of the most reliable analytical methods to estimate bone mineral crystallinity by vibrational spectroscopy, which can be readily implemented in many biomineralization, archeological and orthopedic studies. In particular, we present a step forward in advancing the use of the increasingly utilized ATR FT-IR modality for mineral research.