Winter wheat wholemeal is an important component of the human diet and may be a significant source of antioxidants. The objective of this study was to determine individual phenolic compounds in five winter wheat varieties: ‘Fredis’, ‘Edvins’, ‘94-5-N’, ‘Skagen’, and ‘SW Magnific’ wholemeal, grown according to organic and conventional agricultural practices. Ten phenolic compounds (vanilin, rutin, catechin hydrate, quercetin, p-coumaric acid, ferulic acid, 3.4-dihydroxybenzoic acid, 2-hydroxycinnamic acid, trans (3)-hydroxycinnamic acid, and gallic acid) were detected using high-performance liquid chromatography (Schimadzu Prominence HPLC). Catechin hydrate and quercetin were the main phenolic compounds in the grain of all tested winter wheat varieties. Significant differences (p < 0.05) among the analysed winter wheat cultivars in the concentration of individual phenolic compounds were observed. Concentrations of vanillin in organic and conventional winter wheat wholemeal were significantly lower (0.28 ± 0.02 to 0.65 ± 0.04 µg·g−1 DW), although the differences in the levels of phenolic were not large. The obtained results showed a statistically significant trend (p < 0.05) towards higher levels of phenolic compounds in organic wheat wholemeal samples.