This study reports gas chromatography (GC) combined with Fourier transform infrared (FTIR) spectroscopy to investigate the elution profiles of individual oxime isomers undergoing characteristic interconversion (dynamic chromatography) in GC. The use of a light-pipe FTIR interface enables on-line acquisition of FTIR spectra, which in turn render unambiguous identification of the individual molecules. Here, acetaldehyde oxime and propionaldehyde oxime were chosen for comparison of elution behaviour under varying temperature and carrier flow velocities. The choice of selective responses (wavenumber selectivity), which were relatively stronger for each isomer, enabled display and retracing of the individual isomer over the chromatographic time scale and thus provided characteristic single isomer profiles. Chemometric data analysis using the multivariate curve resolution technique further confirmed this isomer elution profile. Simulation of the spectrum for each isomer allowed comparison with instrument-generated FTIR spectra to confirm the elution order of E and Z isomers. The effect of changing chromatographic parameters (temperature, flow) on interconversion rates and/or extents were studied and the corresponding change in FTIR spectrum intensity was noted. The GC–FID data acquired concurrently with GC–FTIR analyses ratified isomerisation chromatographic profiles.