Evaluation of diagenesis in bioapatite samples is an important step for screening bone and tooth samples for stable isotope analysis to ensure in vivo signatures are obtained. Fourier transform infrared (FTIR) spectroscopy is one tool used to evaluate diagenesis by anthropological geochemists and commonly employs calculating the infrared splitting factor (IR-SF) and carbonate-to-phosphate ratio (C/P). There are three commonly used sample preparation techniques for vibrational spectroscopy: transmission FTIR, attenuated total reflection (ATR), and diffuse reflectance infrared Fourier transform (DRIFT). Each technique characterizes the internal vibrations of particular molecular groups, such as carbonate (CO3) and phosphate (PO4), using different optical properties to detect absorbance bands. Spectra are correlated between techniques using correction equations that account for differences in optical properties. Traditionally, anthropologists have used spectra produced by transmission FTIR to assess diagenesis, most commonly using two indices (IR-SF and C/P); however, recently the ATR and DRIFT techniques have been used as an alternative to transmission FTIR. The spectra produced by the three techniques are thought to be interchangeable in calculating the indices used to assess diagenesis. In this study, we evaluated the interchangeability of the three FTIR techniques by analyzing 452 prehistoric and modern bioapatite samples. Results indicate that IR-SF and C/P values are not equivalent between the three techniques. However, ATR produced more reliable results and was comparable to transmission FTIR. The DRIFT method showed much lower resolution, and did not distinguish between modern and prehistoric bioapatite samples as clearly. •Fourier transform infrared (FTIR) spectroscopy is used to evaluate bone diagenesis.•The commonly used sample preparation techniques are transmission FTIR, ATR, and DRIFT.•Two indices calculated from FTIR spectra, IR-SF and C/P, are used to assess bone diagenesis.•The IR-SF and C/P values are not equivalent between the preparation techniques.•The transmission FTIR, ATR, and DRIFT spectra are not interchangeable.