<p>The cultivation of low-opium varieties of poppy (<i>Papaver somniferum</i> L.) in Central Europe has a very long tradition. The blue seeds, thanks to their delicious taste, have several uses, both in the food industry and culinary practice. However, when seeds are mechanically damaged and/or ground, lipase is released, and a bitter taste develops due to the accumulation of free fatty acids. To prevent hydrolytic rancidity, seeds can be treated with hot steam before grinding. In this way, inactivation of native lipase is achieved. Unfortunately, in some cases, fraudsters misuse the thermostabilization process to remove opium alkaloids from seeds of pharmaceutical poppy varieties, which are then marketed as a food poppy variety. Distinguishing these mislabeled seeds from authentic ones is a rather difficult task. In this study, we have developed a simple Fourier-transform infrared spectroscopy (FT-IR) based strategy for identifying heat-treated poppy seeds. Instead of poppy oil isolation for monitoring the acid value increase, which would occur in case of native seeds, the assessment of spectral changes in the 1730–1690&#xa0;cm^-1 region after poppy seed grinding was employed to recognize thermostabilized seeds. The validation of this novel approach was performed on several poppy seed varieties from various harvest years and also on the set of 108 samples provided by the industrial partner, resulting in 2% of false positives and 7% of false negatives when using the decision criterion of lipase activity factor |LAF| &gt;10%. The working hypothesis was supported by U-HPLC-HRMS/MS analysis of the oil component of the tested seeds.</p>