Pirimiphos methyl is one of the most used compounds among insecticides and acaricides, against pests in post harvest application to cereals, even if it seems to be persistent; however, the milling process could likely represent a phase in which residues significantly decrease. The aim of this work was to comparatively assess the persistence of pirimiphos methyl residues in wheat and oat, after post harvest spray application, and to assess the fate of residues during the processing, by evaluating pirimiphos methyl contamination level in different milling fractions. An analytical method, based on a slightly modified QuEChERS extraction followed by liquid chromatography tandem mass spectrometry (LC-MS/MS) determination was validated: mean recovery was in the range 73% to 92% depending on the spiking level, and precision as RSD ranged from 11% to 16%). The analysis of treated samples revealed that pirimiphos methyl residues were highly persistent: as average, the insecticide persisted at 89% (ranging from 65% in bread making wheat to 107% in oat) after 42 weeks of storage. Furthermore, no differences could be observed between wheat, durum wheat and oat. As far as the impact of the milling process on residues is concerned, pirimiphos methyl contamination was significantly reduced during both cleaning and processing: the insecticide residues in flour were in the range 4-5% of initial contamination, and most of the contamination was related to outer kernel fractions.