This work aimed to study the interaction of sourdough fermentation based on a mixed culture of Lactobacillus plantarum 98a, Lactobacillus sanfranciscensis BB12, Lactobacillus brevis 3BHI with baking process (210–250 °C x 10–20 min) on dietary fiber and phenolic compounds content of bread obtained from immature (milky) and fully ripe flours of modern durum wheat and ancient KAMUT® khorasan wheat whole grains. The fiber in bread was analyzed by enzymatic digestion and the total dietary amount was dependent on genotype and kernel maturation stage. Although insoluble dietary fiber content ranging between 10.26 and 19.25 g/100 g dry base was generally more correlated to KAMUT® khorasan, the soluble fraction (always less than 3.83 g/100 g dry base) was associated to the durum wheat genotype. KAMUT® khorasan bread at fully ripe maturation fermented with sourdough, maximized insoluble dietary fiber content. Sourdough fermentation slightly increased the free flavonoids content while the total flavonoids (obtained by spectrophotometrically analysis) seemed mainly related to each genotype considered (ranged between 39.01 and 56.53 mg/100 g dry base) and its maturation stage. A whole chain strategy based on a combination of agronomic and processing factors was suggested to enhance specific bioactive compounds such as dietary fiber or phenolic compounds.