This study investigated the assistance of ultrasound and Viscozyme L in the extraction of alkaloid and phenolic compounds from cocoa bean (Theobroma cacao L.) shells (CBS). Four variables including ultrasound temperatures (25–75oC), ultrasonic durations (25–65 min); enzyme concentrations (Viscozyme L, 0.5–2.5%), and enzymatic incubation times (10–180 min) were studied separately. As temperature and duration of sonication increased, total phenolic content (TPC), total flavonoid content (TFC) and antioxidant capacity (AC) were enhanced. TPC, TFC, AC ranged from 2.35 to 4.15 g gallic acid equivalents/100 g dry weight (DW); 6.45–10.76 g rutin equivalents/100 g DW; and 14.91–26.19 mol Trolox equivalents/100 g DW, respectively. Sonication at 55oC and 55 min were effective to obtain those polyphenols. Data of Ultra High Performance Liquid Chromatography showed that although amounts of theobromine, catechin, and caffeine extracted from CBS were significantly higher from control samples, however there has been little improvement when high heat and prolonged durations of sonication were employed. Those contents ranging from 1.01 to 1.05 g, 0.59–0.72 and 0.19–0.20 g/100 g DW for theobromine, catechin and caffeine, respectively, were improved with 1.5% Viscozyme L. Meanwhile, incubating the shells with 2.0–2.5% Viscozyme L yielded higher TPC and TFC. Overall, caffeine, AC, TFC, and TPC required 10 min of enzymatic incubation to reach their peak, while 40–50 min were required to achieve the highest theobromine and catechin concentrations.