End product quality of whole wheat bread is affected by many complex parameters. The milling method and chemical composition of bran both affect whole wheat bread quality. When using a centrifugal mill, the combination of low tempering moisture level and high rotor speed produced whole-wheat flour with fine particle size, desirable whole-wheat flour quality, manageable dough, and high loaf volume. Fine bran powder was produced with the combination of low tempering moisture level, low feed rate, and high rotor speed. It was also determined that flour attached to bran affects the bran powder’s temperature, protein content, and starch content. Study of the impact of bran components on whole-wheat bread revealed that fiber (FB) highly impacted gluten quality, farinograph parameters, gassing power, oven spring, loaf volume, and bread crumb protein solubility. FB interacted with other bran components (oils, extractable and hydrolysable phenolics) to increase polymeric protein solubility in bread crumb. Hydrolysable phenolics (HP) improved the farinograph stability. However, the interaction of FB with other components decreased bread loaf volume, especially for the interaction of FB-HP. The baking method and the type of wheat used for whole-wheat bread are also important factors to evaluate whole-wheat bread quality. Sponge-and-dough (SpD), straight dough (StD), and no-time dough (NoD) methods were compared. StD had the highest variation in baking mix time, baked weight, crumb grain score, and symmetry score compared to other baking methods. The StD method was the most sensitive method to distinguish variation in whole-wheat flour samples. Location and cultivar effects were investigated for whole-wheat bread quality. Twenty-one hard red spring wheat cultivars grown at 6 locations across North Dakota were evaluated for whole-wheat bread quality. Location contributed 89% to the variability in whole-wheat baking absorption. Cultivar contributed 47% and 41% to the variability in whole-wheat loaf volume and loaf symmetry, respectively. Loaf volume and crumb color were largely under genetic control, and breeders can aim at high loaf volume in whole wheat bread made from hard spring wheat. Overall, whole-wheat flour and bread quality are greatly affected by: milling method, bran composition, baking method, as well as the environment and genotype.