Approximately 500 thousand tons of cocoa bean shells (CSs) are generated annually and treated as waste. However, their composition is of great nutritional, technological, and economic interest due to their dietary fiber (46.4 to 60.6%), protein (11.6 to 18.1%), and lipid contents (2 to 18.5%), as well as the presence of flavonoids and alkaloids. Thus, this study aimed to obtain CS flour by milling the CSs, characterizing the flour according to its chemical composition and functionalities, and then applying it in the production of cookies, substituting a wheat flour portion (10, 20, 30, and 40%) with CS flour. Cookies were characterized in terms of water, lipids, proteins, phenolic (PC), and total flavanol (FLA) contents, and specific volume (SV), hardness (H), and L*, a*, and b color scale parameters. Increasing the amount of CS showed positive results, as the cookies were enriched with PC (0.68 to 2.37 mg gallic acid equivalents/g of sample) and FLA (0.10 to 0.19 mg epicatechin equivalents/g of sample) but increased hardness (353 to 472 N). By associating the responses, it was concluded that the wheat flour replacement with 30% CS presented values of PC and FLA 3 and 1.6 times higher than the control and could be a formulation of interest to consumers.