Maya nut (Brosimum alicastrum) is a novel food with high nutritional value. This research aimed to evaluate the nutritional and antioxidant properties of Maya nut flour (MNF) made from seeds dried by different methods (sun-dried and using hot air at 45 °C and 60 °C) to explore its incorporation into cookies and evaluate its nutritional and functional properties. The naturally sun-dried flour (NF) had the highest content of ash (3.64 ± 0.11 g/100 g), protein (6.35 ± 0.44 g/100 g), crude fiber (6.75 ± 0.29 g/100 g), and functional properties (water and oil absorption). The color of the flour was affected by the different drying methods. While the drying methods influenced the total polyphenolic content (TPC) and antioxidant activity (AA) of MNF, they did not affect the morphology of the native starch or generated important molecular-structural changes. The substitution of 60% of wheat flour with NF in the cookie’s formula increased the protein and fiber content, whereas 20% substitution increased its AA. MNF is a source of protein, dietary fiber, micronutrients, and functional compounds that can enrich cookie formulations.