Demand for the ancient wheats spelt and emmer has increased in recent years as consumers associate these wheats with attributes such as regional, better tasting and sustainable. However, compared to wheat, spelt and emmer have more difficult processing characteristics due to the formation of sticky and soft doughs. Gluten is mainly responsible for the good baking properties of wheat. Based on what is known so far, not all of the causes for the poorer baking properties of spelt and emmer can yet be explained. At the molecular level, the cross-linking of the gluten proteins by disulfide bridges is decisive. This crosslinking can be prevented by free thiols, which act as so-called terminators. Baking aids are already used as standard for wheat and can improve baking properties, e.g., by removing the free thiols. In addition to chemical and enzymatic baking auxiliaries, special dough management and the use of sourdoughs also improve baking properties. At the moment, there is a lack of systematic studies on how the free thiol content differs in spelt and emmer compared to wheat and to what extent these differences can be influenced by chemical and enzymatic baking aids, the use of sourdough and by special dough management. By studying these structure-activity relationships, the reasons for the poorer baking properties of spelt and emmer will be elucidated at the molecular level. The knowledge will be used to improve the baking properties of spelt and emmer on this basis. The results will be of particular benefit to artisanal bakeries and SMEs in the grain processing industry, as they can positively influence the baking properties of spelt and emmer either through special techniques or the use of baking aids in order to obtain high-quality products.