In this work, Fourier transform infrared spectroscopy (FTIR) is used to monitor perfluorocompound process emissions during in situ cleaning of a plasma enhanced chemical vapor deposition chamber. Gas mixtures containing CF4, C2F6, C3F8, SiF4, and COF2 are identified and quantified simultaneously using FTIR. The results of this study show that the lower rate and higher utilization of etch gas during a C3F8 chamber cleaning process can contribute to reductions in net perfluorocompound emissions relative to a C2F6 cleaning process of similar duration. This work also demonstrates that FTIR spectroscopy can provide information which is necessary to support the development of alternative chamber cleaning chemistry. In this way, monitoring methods based on FTIR spectroscopy are valuable to the semiconductor industry’s perfluorocompound emission reduction objectives.