Plant biodiversity preservation is one of the most important priorities of today’s agriculture. Wheat (Triticum spp. L.) is widely cultivated worldwide, mostly under a conventional and monovarietal farming method, leading to progressive biodiversity erosion. On the contrary, the evolutionary population (EP) cultivation technique is characterized by mixing and sowing together as many wheat genotypes as possible to allow the crop to genetically adapt over the years in relation to specific pedoclimatic conditions. The objective of this study was to assess the nutritional, chemical and sensory qualities of three different breads obtained using different organic EP flours, produced following a traditional sourdough process and compared to a commercial wheat cultivar bread. Technological parameters, B-complex vitamins, microelements, dietary fibre and phenolic acids were determined in raw materials and final products. Flours obtained by EPs showed similar characteristics to the commercial wheat cultivar flour. However, significant differences on grain technological quality were found. The breads were comparable with respect to chemical and nutritional qualities. Overall, the sensory panellists rated the tasted breads positively assigning the highest score to those produced with EPs flours (6.75–7.02) as compared to commercial wheat cultivar-produced bread (cv. Bologna, 6.36).