Wheat-based short-dough cookies are considered low nutritional value foods because their recipes are high in fat and sugar. The aim of this study was to investigate the effects of replacing part of the wheat flour (WF) with different types of malted barley flour (MBF), while reducing sucrose in the recipe, in order to produce cookies with increased nutritional value, enhanced functional properties, and acceptable technological and sensory characteristics. Three types of brewer’s MBF (Pilsen, Amber, and Black) were used to replace WF in amounts of 20, 40, and 60%, while simultaneously reducing the addition of sucrose. Sucrose was added at levels of 66.6, 33.3, and 0% of the original standard recipe. MBF mitigated the effects of the reduced sucrose addition, likely due to its own high sugar content derived from barley malt. Snapping force determined with a texture analyzer decreased proportionally to sucrose reduction and MBF addition, indicating a softer texture of the cookies. MBF significantly increased the total phenolic content (TPC) and antioxidant activity (AOA) of the cookies. The results of the sensory analysis showed that cookies with Pilsen MBF and Amber MBF had a pleasantly sweet and rich flavor, while the addition of Black MBF produced an exaggerated bitter flavor and a nutty roasted aroma. The results suggest that different types of brewer’s MBF can be successfully used to produce functional cookies with reduced sucrose addition.