Glow discharge (GD) source gained an increased level of attention in relation to the analysis of volatile organic compounds (VOCs) since past work showed that this soft ionization method allowed direct analysis of VOCs with minimal fragmentation, however, the issue of fragmentation was not previously studied in detail. The aim of the present work was to investigate the effect of discharge conditions on VOC fragmentation in the system consisting of the cell with pulsed glow discharge and a time-of-flight mass spectrometer. Ionization of VOCs of different classes (hydrocarbons, alcohols, esters, and carboxylic acids) was investigated. A copper cathode with flat geometry was used. VOCs were ionized in the afterglow of short pulse glow discharge in the air. The use of discharge afterglow significantly reduces or eliminates the effects of ionization mechanisms other than Penning process, in particular, electron ionization. This significantly reduced VOC fragmentation and provided rather low limits of detection. Specific cluster formation was observed for alcohols and esters, which may facilitate their identification.