The aim of the study was to evaluate the effect of extruded germinated black bean cotyledon flour (EBB) as a substitute of nixtamalized blue maize (NBM) flour on proximal composition, physicochemical characteristics, protein, starch digestion performance, and sensory analysis with a just about right (JAR) scale of NBM cookies. A ratio of 82.5:7.5 (NBM:EBB) decreased the viscosity of the flour mixtures, thus decreasing the spread factor to 15.44%. The EBB significantly increased the protein content and its digestibility 17.43 and 3.65%, respectively. A relative higher amount of slowly digestible starch and remaining RS was found in the substituted EBB cookies. Furthermore, EBB substitution showed a significantly lower predicted GI than that elaborated solely with NBM. The JAR scale showed that cookies substituted with EBB7.5 were evaluated with an ideal texture (70.0%). Overall, considering functional and nutritional properties, NBM plus EBB could be a good alternative to produce high‐protein cookies.