The paper presents the effect of conventional (use of NPK mineral fertilizers and pesticides) and organic (no use of agrochemicals) farming systems on selected parameters of antioxidant properties of winter wheat, spring barley and oat grain. The research was carried out during the period 2017–2019 at the Czesławice Experimental Farm (central Lublin region, Poland) on loess soil (second quality class). The aim of the research was to evaluate the functional (antioxidant) properties of winter wheat, spring barley and oat grain in whole grain and its milling fractions (dehulled grain, flour and bran). The reduction potential (Fe+3 → Fe+2 ), the ability to eliminate the free DPPH• radical and the total antioxidant potential in the β-carotene/linoleic acid system were determined. Polyphenol content was also determined using Folin–Ciocalteau reagent. The organic system did not significantly increase the antioxidant properties of cereal grains compared to the conventional system. Under organic farming conditions, oat grain was characterised only by the most favourable antioxidant properties. A highly statistically significant correlation was found between total polyphenol content and DPPH• free radical quenching capacity, especially for oat and barley in the organic system. The closest correlations were for the fractions of bran and whole grain. Dehulling of grain, with the exception of oat grain, irrespective of the farming system, resulted in a significant deterioration of the antioxidant potential of grain extracts. In summary, the study showed that the bran obtained from oat grown under an organic system had the strongest antioxidant activity.