Flaxseed has been recently studied for the formulation of healthy functional foods that are also useful for the prevention of chronic diseases. In this context, the production of sourdough bread fortified with different percentages of flaxseed cake was performed and the interactions among the bioactive compounds derived from both sourdough and flaxseed cake were investigated. The organoleptic properties as well as nutraceutical and chemical characteristics regarding pH, ethanol, lactic and acetic acid content, fatty acids profile, the concentration of total polyphenols, antioxidant capacity, and aroma volatile organic compounds were determined to evaluate the efficacy of leavening in the different matrices in comparison with the traditional bread. The results obtained demonstrated that flaxseed cake-enriched sourdough bread can represent a potential vehicle for bioactive compounds with the possibility of obtaining high-quality products with improved nutritional profiles and desired health attributes. Furthermore, the bread obtained with the addition of 7.5% of flaxseed cake was individuated as the best formulation to produce sourdough bread fortified with flaxseed cake by the overlap between three series of information coming from physical-chemical, nutritional, and sensorial analyses. In conclusion, in the operating conditions adopted, the use of flaxseed cake could represent a viable alternative for the production of fortified bread based on sourdough technology.