Two analytical techniques - online Gas Chromatography coupled with Flame Ionization Detector (often used method for VOCs monitoring) versus Selected Ion Flow Tube coupled with Mass Spectrometry (a more recent technique based on direct mass spectrometry) - were compared in association to an ozone-based gas treatment. Selecting aldehydes as the representative VOCs, their concentrations were monitored during ozonation experiments by both techniques in parallel. Contradictory results were obtained in the presence of ozone. Aldehydes were up to 90% removed due to a reaction with ozone according to GC/FID analysis, whereas with SIFT/MS, aldehydes concentration remained at the same level during the experiments regardless of the ozone presence. In addition, it was demonstrated that the apparent aldehydes removal was affected by GC injector temperature, varying from 90% (when it was at 250 °C) to 60% (at 100 °C). Meanwhile, even when the ozonation reactor was heated to 100 °C, no aldehydes conversion was evidenced by SIFT/MS, suggesting that the GC injector temperature was not the only interference-causing parameter. The ozone-aldehyde reaction is probably catalyzed by some material of GC injector and/or column. An ozone-GC interference was therefore confirmed, making unsuitable the use of GC/FID with silicone stationary phase to monitor aldehydes in presence of high concentrations of ozone (at least 50 ppmv). On the other hand, SIFT/MS was validated as a reliable technique, which can be employed in order to measure VOCs concentrations in ozonation processes.