Gluten-related disorders, including celiac disease and non-celiac gluten sensitivity, are growing worldwide. The only treatment for both disorders is a lifelong gluten-free diet. However, gluten-free foods are generally poorer in nutrients, less healthy, and have a high cost. Sorghum and cowpea are gluten-free grains with high levels of phenolic compounds (PC) and a low cost. Their phenolic profile is structurally different; thus, the blend of both can provide synergistic/complementary health benefits to the final product. This study analyzed the effect of baking process and the blend of cowpea flour (CP) and sorghum bran (SB) on the levels of PC, resistant starch (RS), neutral detergent fiber (NDF), and antioxidant capacity (AC) of gluten-free cookies. Eleven rice or cowpea cookie formulations were made with or without white sorghum bran (WSB) or black sorghum bran (BSB). Baking increased the extractability of PC, AC, and the NDF of almost all formulations. The PC and AC were, respectively, about twice and 3-5 times higher in cookies containing BSB compared to the others. There was a minor effect of WSB on the PC and AC. Although there were losses, the retention of RS of cookies after the baking process was between 49.8 and 92.7%. Sorghum bran has excellent potential for use as a functional ingredient in healthy food production. The combined CP and SB have great potential to improve the nutritional and functional properties of gluten-free products, especially the PC, RS, and NDF contents.