Compositional and Metabolomic Characterization of Major On-Farm Side Streams and Derived Products of Industrial Fine-Flavor Cocoa Processing

Abstract The fine-flavor cocoa agro-industrial chain generates on-farm side streams with distinct origins and processing histories, yet their compositional diversity remains insufficiently characterized under industrial conditions. Here, we performed an integrated compositional and metabolomic characterization of cocoa pod husk, cocoa pulp juice, and cocoa syrup generated within a large-scale monoclonal fermentation system (Luker 40; ∼500 kg per fermentation box) operating within an industrial fine-flavor cocoa production system exceeding 73,000 tons annually. Metabolomic characterization was performed using three independent industrial production batches as biological replicates (n = 3), whereas proximate and mineral analyses were performed on composite samples prepared from the three batches. Mineral composition showed the largest relative differences among matrices, with cocoa syrup reaching an ash content approximately 12 times that of cocoa pulp juice. Complementary LC-MS and GC-MS analyses enabled the annotation of 82 metabolites (46 by LC-MS and 36 by GC-MS), revealing distinct matrix-resolved profiles, including caffeic acid, epicatechin, and procyanidin B1 in cocoa pod husk; glutamine, glutathione, and indole carboxaldehyde in cocoa pulp juice; and N-(deoxyfructosyl) amino acid derivatives in cocoa syrup. To our knowledge, this is the first joint compositional and metabolomic description of a thermally concentrated, fermentation-derived cocoa syrup together with prefermentation cocoa pulp juice recovered from the same production batches. These results provide a compositional baseline for subsequent targeted quantification, extraction/recovery, and functional validation, supporting the rational prioritization of cocoa side streams and derived products for future valorization studies.