Whole-wheat flour of purple wheat varieties contains anthocyanins and other phenolic compounds with high antioxidant activity, which makes it a potential raw material for functional foods. The content and composition of phenolic compounds in whole-wheat flour depends on the genotype and weather conditions; in the bread, however, they also depend on the bread-making technology. This article offers a comparative analysis of phenolic compounds in purple whole-wheat flour and bread baked from this flour. The study featured purple soft spring wheat (Triticum aestivum L.) of two varieties, Nadira and Line 193, which were harvested in 2016 and 2017, and corresponding bread samples. The antioxidant activity and phenolic content were measured spectrophotometrically while the qualitative analysis relied on the method of high-performance liquid chromatography (HPLC). In the hot and dry year of 2016, the content of bound phenolic acids reached 2.0–2.4 mg/g dry weight in the flour of both genotypes. In the cool and humid year of 2017, the content of anthocyanins in the Nadira flour increased by 2.7 times and amounted to 0.65 mg/g dry weight. However, the corresponding bread sample had a much lower phenolic content: soluble phenolics were halved, anthocyanins dropped by 3–4 times, and bound phenolic acids went down by 7–17 times. The content of bound phenolic acids in the flour correlated positively with the content of free phenolic acids in the bread. The HPLC analysis revealed an increase in the content of free hydroxycinnamic acids in the bread: p-coumaric acid was the most abundant and amounted to 0.14–0.22 mg/g dry weight. Conventional State Standard 27669-88 for bread making resulted in a total decrease in anthocyanins, bound phenolic acids, and most free phenolics. Therefore, this technology cannot be applied to functional bread. The results can help develop a breadmaking technology for purple wheat varieties.