Mushroom stems are the main waste generated during mushroom production, which are still treated as residue, although their nutritional and bioactive composition is very similar to that of the fruiting body. It is therefore a waste with great potential to be transformed into a high-value-added by-product as a functional ingredient or incorporated directly into formulations to develop new functional foods. This chapter provides a guide for the production of functional flours from mushroom stem residues, through a drying process (dehydration or freeze-drying), to be incorporated into basic bakery doughs, thus enhancing their nutritional profile and health-promoting properties.