The present study was aimed to investigate the variation of stable isotopic ratios of carbon, nitrogen, hydrogen, and oxygen in wheat kernel along with different processed fractions from three geographical origins across 5 years using isotope ratio mass spectrometry (IRMS). Multiway ANOVA revealed significant differences among region, harvest year, processing, and their interactions for all isotopes. The region contributed the major variability in the δ13C ‰, δ2H ‰, δ15N ‰, and δ18O‰ values of wheat. Variation of δ13C ‰, δ15N ‰, and δ18O ‰ between wheat whole kernel and its products (break, reduction, noodles, and cooked noodles) were ˂0.7‰, and no significant difference was observed, suggesting the reliability of these isotope fingerprints in geographical traceability of wheat‐processed fractions and foods. A significant influence of wheat processing was observed for δ2H values. By applying linear discriminant analysis (LDA) to the whole dataset, the generated model correctly classified over 91% of the samples according to the geographical origin. The application of these parameters will assist in the development of an analytical control procedure that can be utilized to control the mislabeling regarding geographical origin of wheat kernel and its products.