The metabolic syndrome is a cluster of conditions that occur together, increasing the risk of chronic diseases such as obesity, type II diabetes, or cardiovascular disease. Nutritional interventions improving inflammation, bioenergetics, and oxidative stress are proposed as effective tools in preventing metabolic syndrome. The cocoa shell is a by-product generated in large amounts during cocoa production. This by-product contains alkaloids and phenolic compounds as main compounds and has been investigated as an anti-obesity and anti-diabetic agent. Here, we used network pharmacology to explore the potential mechanism of the phytochemicals from the cocoa shell. We searched the cocoa shell's phytochemical composition, and oral bioavailability and drug-likeness were screened. We predicted the cocoa shell phytochemicals' targets and used different databases to search for compound-protein and compound-gene interactions, and then protein-protein interaction networks were constructed. Moreover, pathway enrichment analysis was performed, and biological processes and signaling pathways were identified and illustrated through bioinformatics analyses. Theobromine, caffeine, procyanidin B2, (−)-epicatechin, (+)-catechin, and protocatechuic acid were identified in the cocoa shell as main components. Those phytochemicals were associated with inflammation- (TNF-α, NF-κB, JNK), oxidative stress (CAT, SOD), obesity- (adiponectin, leptin, FASN, PPAR-α), and diabetes- (insulin, AKT,) related pathways. Results demonstrated that cocoa shell phytochemicals could modulate multiple biological processes and signaling pathways in a multimechanistic manner. Hence, cocoa shell consumption could support the nutritional prevention of metabolic syndrome. Future in vivo and clinical investigations will be needed to validate this potential nutraceutical and healthy ingredient's effects and mechanisms.