Cocoa pod husks (CPH) and cocoa bean shells (CBS) are the main by-products of the cocoa industry and a source of bioactive compounds. These residues are not completely used and thrown in the fields without any treatment, causing environmental problems. Looking for a holistic valorization, the aim of this work was first to deeply characterize CPH and CBS in their chemical composition, amino acid, and fatty acid profiles, as well as their application as antioxidants. CBS had a high level of protein (17.98% DM) and lipids (16.24% DM) compared with CPH (4.79 and 0.35% DM respectively). Glutamic acid and aspartic acid were the predominant amino acids. The total phenolic compounds (TPC) detected in the ethanolic extracts of CPH and CBS were similar to pyrogallol as the main detected polyphenol (72.57 mg/L). CBS ethanolic extract showed a higher antioxidant activity than CPH. Both extracts increased the oxidation stability of soybean oil by 48% (CPH) and 32% (CBS). In addition, alkaline pretreatment of CPH was found suitable for the release of 15.52 ± 0.78 g glucose/L after subsequent saccharification with the commercial enzyme Cellic®. CTec2. Alkaline hydrolyzed and saccharified CPH (Ahs-CPH) was assessed for the first time to obtain polyhydroxy alkanoate (PHAs) and bioethanol. Ahs-CPH allowed the growth of both Cupriavidus necator DSM 545 and Saccharomyces cerevisiae Fm17, well-known as PHA- and bioethanol-producing microbes, respectively. The obtained results suggest that such agricultural wastes have interesting characteristics with new potential industrial uses that could be a better alternative for the utilization of biomass generated as million tons of waste annually.