Photoinitiators are used to promote the polymerization process during the curing of varnishes or inks on cartonboard packaging. Depending on storage conditions and shelf life, these substances are able to migrate through the packaging layer into the foodstuff. This type of contamination phenomenon is therefore becoming a critical issue in terms of food safety. In order to tackle this problem, a fast and selective method was developed for the determination of benzophenone and three methylbenzophenone isomers in cereal-based foodstuffs and their cardboard packaging. Food samples or packages were efficiently extracted by pressurized liquid extraction using acetonitrile, and the extracts were directly injected onto the analytical system. The analysis was performed by multidimensional gas chromatography–mass spectrometry using a heart-cutting approach to reduce the background noise from complex matrices. The strategy employed two distinct cuts each containing its proper deuterated internal standard leading to accurate quantification. By integrating a cryofocusing effect, an enhancement in signal/noise ratio was achieved by a factor >10, which markedly decreased the sensitivity threshold. Moreover, baseline separation of the critical isomers allowed their unequivocal determination. The method was fully validated on cereal-based foodstuffs based upon an analysis of variance, and excellent performances were obtained at the decision limit making this method well suited for official food controls.