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One of the main by-products in cocoa industry is the cocoa bean shell (CBS), which represents approximately 12–20% of the bean. This product has been suggested as a food ingredient because of its aroma and high dietary fiber and polyphenol contents. The purpose of this work was to evaluate the effects of the CBS particle size and extraction methods on the chemical composition and consumer acceptance of a functional beverage, in order to find the best combination of technological parameters and health benefits. Five particle sizes of CBS powder and six home techniques were used for beverage preparation. The influence of these factors on the physico-chemical characteristics, methylxanthine and polyphenolic contents, antioxidant and antidiabetic properties, and consumer acceptance was evaluated. Total phenolic content values up to 1803.83 mg GAE/L were obtained for the beverages. Phenolic compounds and methylxanthines were identified and quantified by HPLC-PDA. These compounds may be related to the high antioxidant capacity (up to 7.29 mmol TE/L) and antidiabetic properties (up to 52.0% of α-glucosidase inhibition) observed. Furthermore, the consumer acceptance results indicated that CBS may represent an interesting ingredient for new functional beverages with potential health benefits, reducing the environmental and economic impact of by-product disposal.