To provide people with celiac disease with nutrient-rich gluten-free foods, this study aimed to produce cookies based on buckwheat and baobab flours, which were then subjected to nutritional, phytochemical, and sensory analyses. Results demonstrate that baobab flour (BF) and buckwheat flour (BWF) work together to enhance the nutritional properties of the cookies, in that nutrients that BWF is deficient in, BF provides sufficiently, and vice versa. BF is rich in minerals and carbohydrates, while BWF contains comparatively higher fat and protein levels. As for macro- and micro-elements, potassium (K) is the predominant macro-element in BF and BWF, with 13,276.47 ± 174 mg/kg and 1255.35 ± 58.92 mg/kg, respectively. The polyphenol content is higher in BF than BWF, at 629.7 ± 0.35 mg/100 g as opposed to 283.87 ± 0.06 mg/100 g. Similarly, the total flavonoid content and antioxidant activity of BF was greater than that of BWF, while BF exhibited 213.13 ± 0.08 mg/100 g and 86.62 ± 0.04%, in contrast to BWF, which had 125.36 ± 1.12 mg/100 g and 79.72 ± 0.01%, respectively. BF significantly enhanced the phytochemical composition of the cookies, with the richest sample being BBC3 containing 30% baobab. Buckwheat and baobab have the most abundant phenolic compounds of rutin and epicatechin, respectively. About the analysis of sensory attributes of the cookies, the partial substitution of BWF by BF of up to 20% (BWF3) significantly increased the scores for all attributes. Indeed, the appearance (physical aspect of the cookie: whether it is firm or not) and color (influence of baobab addition on cookie coloration) of the cookies were significantly improved with the addition of BF of up to 20%, but above 20% they were less appreciated. Similarly, up to 20% BF, the texture, flavor, and overall acceptability of the cookies were significantly improved. Taste, on the other hand, was not significantly improved, maybe due to the acidic taste provided by the baobab.