A rapid screening method for the investigation of plasma-induced chemical modifications was developed by analyzing cysteine using Fourier Transform Infrared (FTIR) spectroscopy. Cysteine is a key amino acid in proteins due to the presence of a thiol group which provides unique structural features by offering the possibility to form disulfide bonds. Its chemical composition makes cysteine a well-suited model for the investigation of plasma-induced modifications at three functional groups—the amino, the carboxyl and the thiol group—all highly abundant in proteins. FTIR spectroscopy is present in most physical laboratories and offers a fast way to assess changes in the chemical composition of cysteine substrates due to plasma treatment and to compare different treatment conditions or plasma sources with each other. Significant changes in the fingerprint spectra of cysteine samples treated with a dielectric barrier discharge (DBD) compared to untreated controls were observed using a FTIR spectrometer. The loss of the thiol signal and the simultaneous increase of bands originating from oxidized sulfur and nitrogen species indicate that the thiol group of cysteine is modified by reactive oxygen and nitrogen species during DBD treatment. Furthermore, other plasma-induced modifications, such as changes of the amino and carbonyl groups, could be observed. Complementary mass spectrometry measurements confirmed these results.