The data obtained with a polar or non-polar gas chromatography (GC) column coupled to ion mobility spectrometry (IMS) has been explored to classify Iberian ham, to detect possible frauds in their labelling. GC-IMS was used to detect the volatile compound profile of dry-cured Iberian ham from pigs fattened on acorn and pasture or on feed. Due to the two-dimensional nature of GC-IMS measurements, great quantities of data are obtained and an exhaustive chemometric processing is required. A first approach was based on the processing of the complete spectral fingerprint, while the second consisted of the selection of individual markers that appeared throughout the spectra. A classification rate of 90% was obtained with the first strategy, and the second approach correctly classified all Iberian ham samples according to the pigs' diet (classification rate of 100%). No significant differences were found between the GC columns tested in terms of classification rate.