Breeding programs for purple wheat are underway in many countries but there is a lack of information on the effects of Pp (purple pericarp) genes on agronomic and quality traits in variable environments and along the product chain (grain-flour-bread). This study was based on unique material: two pairs of isogenic lines in a spring wheat cv. Saratovskaya-29 (S29) background differing only in Pp genes and grain color. In 2017, seven experiments were conducted in Kazakhstan, Russia, and Turkey with a focus on genotype and environment interaction and, in 2018, one experiment in Turkey with a focus on grain, flour, and bread quality. The effect of environment was greater compared to genotype for the productivity and quality traits studied. Nevertheless, several important traits, such as grain color and anthocyanin content, are closely controlled by genotype, offering the opportunity for selection. Phenolic content in purple-grained lines was not significantly higher in whole wheat flour than in red-colored lines. However, this trait was significantly higher in bread. For antioxidant activities, no differences between the genotypes were detected in both experiments. Comparison of two sources of Pp genes demonstrated that the lines originating from cv. Purple Feed had substantially improved productivity and quality traits compared to those from cv. Purple.