Background and ObjectivesEffects of the physicochemical properties of buckwheat flour (BKF), quinoa flour (QF), proso millet flour (PMF), and whole wheat flour (WWF) were evaluated in a pancake product made with unbleached fine wheat pastry flour (FWF). Pancakes were formulated with 25%, 50%, 75%, and 100% (w/w) substitution levels. FWF was used as the control.FindingsThe flours varied in composition, affecting their functional properties. BKF was characterized by high total dietary fiber (TDF), FWF had the highest starch content, WWF had the highest protein content, and PMF had the highest peak and onset temperature. The influential functional properties on pancake quality were the content of TDF and insoluble dietary fiber, as well as the water and oil holding capacity. Due to the rapid cooking time in pancakes, the PMF starch did not gelatinize adequately, likely due to the amylose content or shape and size of the starch, resulting in a low‐hardness pancake without a continuous matrix. When a pancake was prepared with partial pregelatinized PMF, the pancake had a continuous matrix.ConclusionBK, QF, and WWF can be incorporated into pancake formulations without flour modification. PMF must be modified before usage in a pancake application to ensure that a continuous matrix is formed.Significance and NoveltyThis research sheds light on the importance of considering the functional properties of alternative grains in baked product formulations. Nonetheless, further information was found on PMF starch gelatinization in pancake applications.