We present a new approach to determine in situ CO2 and H2O concentrations in apatite via attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). Absolute carbon and hydrogen measurements by nuclear reaction analysis (NRA) and elastic recoil detection (ERD) are used to calibrate ATR-FTIR spectra of CO2 and H2O in apatite. We show that CO2 and H2O contents in apatite can be determined via linear equations (r2 > 0.99) using the integrated area of CO2 and H2O IR absorption bands. The main benefits of this new approach are that ATR-FTIR analyses are non-destructive and can be conducted on polished sample material surfaces with a spatial resolution of ~ 35 μm. Furthermore, the wavenumber of the phosphate IR absorption band can be used to determine the crystallographic orientation of apatite, which allows for accurate quantification of CO2 and H2O in randomly orientated apatite grains. The limit of quantification of H2O in apatite is ~ 400 ppm and ~ 100 ppm for CO2. Via two examples, one from a carbonatite and one from a metasedimentary rock, we show that this new technique opens up new possibilities for determining volatile concentrations and behavior in a wide range of hydrothermal, igneous, and metamorphic systems.