The study aimed to determine variations in macro/microelements, nutrients and bioactive components in grain and stone-milled fractions of common and Tartary buckwheat cultivated over three consecutive years. Whole grain were milled to obtain several fractions: light flour, semolina, three or four bran fractions, and hulls. Dry matter, crude protein, crude fat, macro- and microelements, total antioxidant capacity, rutin and quercetin contents, and compounds with antioxidative potential were determined. Crude protein in buckwheat samples ranged from 2.9% to 35.7%, and crude fat from 0.2% to 10.1%. Bioactive compounds were significantly higher in Tartary buckwheat samples, especially for semolina and bran fractions. The multi-elemental compositions of these buckwheat species were comparable, while the differences between the milling fractions varied considerably for K, P, Mg, S, Fe and Zn. Principal component analysis for 20 parameters derived from 45 samples showed good discrimination for buckwheat whole grain, light flour and hulls for both species, for Tartary buckwheat bran and semolina, and for common buckwheat bran and semolina. The profiles of compounds with antioxidant potential were significantly different between the buckwheat species, as well as for hulls and bran fractions compared with the other fractions. In general, harvest year did not have any significant impact on any of the parameters analysed. •Traditional stone milling was applied for common and Tartary buckwheat whole grains.•Three years whole grains and milling fractions were analysed for several nutrients.•Bioactive compounds were higher in semolina and bran fractions of Tartary buckwheat.•Multi-elemental content of common and Tartary buckwheat fractions was comparable.•HPLC-ECD was used to differentiate buckwheat species and milling fractions.