The use of zero-waste processes to integrate food-waste valorisation into the circular economy equation is currently one of the hottest topics in sustainability research. This goal is still far from being fully achieved despite the release of a number of patents and papers that deal with the topic. The present work aims to valorise cocoa shells, one of the main by-product of the roasting process, in order to enhance the effective extraction of high added value compounds by means of green protocols. The high potential added value of the residual waste has been demonstrated via a direct analytical comparison of extracts and bean composition. A range of raw matrix extraction procedures have been investigated in order to define the best solvent and technology; ultrasound (US) and hydrodynamic cavitation (HC) were compared with conventional methods. The high-energy microenvironments generated by cavitation substantially promote fast biomass deconstruction with low energy consumption. The optimized protocol couples a HC reactor with a ternary water/ethanol/hexane mixture, simultaneously providing a hydrophilic product, which is rich in methylxanthines and polyphenols, and a lipid layer. Sequential milling and sieving pretreatment provided an enriched shell fraction via the partial removal of husk fibres (54.45 vs. 81.36 w/w % total fibres). The disposal of the latter reduces mass balance, but is rerouted into animal feedstock components and crop mulching. The protocols herein reported produce valuable extracts, which are rich in antioxidant flavanols (catechins and epicatechins), theobromine (32.7 ± 0.12 mg/g shells), caffeine (1.76 ± 0.08 mg/g shells) and cocoa butter, in a simple and easy manner. This new valorisation process afforded 20.5 w/w % and 15.8 w/w % hydrophilic and lipophilic fractions, respectively, when scaled up to function in a pilot flow reactor. The fatty acids, obtained in remarkable yield (forming the 96.4 w/w % of the total light part) well match the commercial cocoa butter profile. The antioxidant extract shows an impressive total phenolic content of 197.4 mg/g extract (gallic acid eq.), with a radical scavenging activity of 62.0 ± 3.1 μg/mL (expressed in DPPH EC50). This work should facilitate industrial design for the convenient recovery of cocoa by-products as part of a zero-waste strategy.