In recent years, the attention of farmers, bakers and consumers towards ancient wheat species has been increasing. Low demands of pedo-climatic growth factors, the suitability for organic cultivation along with their high nutritional quality and their content in pro-health compounds make them extremely attractive for bakers and modern consumers, equally. On the other hand, in recent years, sourdough has gained attention due to its ability to produce new functionally active molecules with higher bioaccessibility and thus to produce bread with enhanced nutritional quality. This paper highlights the relevant nutritional profile of einkorn, spelt, emmer and Khorasan which could lead to bread with improved textural, sensorial, microbial and nutritional characteristics through sourdough fermentation. The ancient wheat species could be used as promising substitutes for common wheat flour for the design of innovative types of bread, even for special needs.