This study was undertaken (i) to optimise and validate a suitable method for multi-element determination in cereal products and (ii) to evaluate multi-element content differences in commercially available conventional vs. organic wheat flours. Presented ICP-MS method is simple and accurate for the determination of eighteen elements in cereal food. Obtained results show differences in metal content between conventional and organic wheat flours and confirm that both types of production are well within the toxicological safety limits regarding the metal contents. The significant differences among conventional vs. organic wheat flours were obtained for As, Cd, Cr, Fe, Mg, Mo, Ni and V. Toxic metals (Al, As, Cd and Pb) input was higher in conventional compared with organic wheat flours. However, further and long-term research is needed to clearly underline the effects of organic agricultural practice on the quality of food products.