Gluten -free sugar cookies were made from amaranth (Amaranthus caudatus) and navy bean flours of different ratios. The physical properties of flour blends, dough, and cookies were evaluated. This study found that navy bean and its blends with amaranth had greater water holding capacity (WHC) than that of wheat flour. The increased WHC was observed as the amount of navy bean flours increased in blends. The amaranth flour had the highest water soluble index (WSI) and pasting viscosities. The WSI, pasting viscosities and rheological elastic properties of composites were improved by amaranth flour. Differences were also found in geometrical and textural properties of the doughs and cookies. The cookies made from flour blends have lower width and spread factors; however, they had higher thickness and volume resulting in higher yield compared to wheat flour. Overall, the cookies made by amaranth, navy bean, and their blends were rated “acceptable” in color, flavor, texture, and overall acceptability in the sensory study. The flavorings of vanilla, cinnamon, and almond extracts improved sensory scores of cookies made from blends, making them indistinguishable from cookies using wheat flour. This study suggested that the amaranth-navy bean blends could be good gluten-free candidates for health-promoting food products.