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Cocoa bean shells (CBS), generated during Theobroma cacao L. processing, are by-products rich in methylxanthines and phenolic compounds. Even with a wide range of bioactive compounds, it remains underexplored. This work developed an integrated strategy to select bio-based solvents and intensify the recovery of theobromine, caffeine, catechin, epicatechin, and procyanidin B2. COSMO-RS was first applied to predict the co-solubilization of theobromine and epicatechin in solvents classified as recommended or problematic by the CHEM21 guide. The most promising solvents were experimentally validated by solid–liquid extraction, and their extraction performance was combined with environmental, health, and safety criteria using TOPSIS. This strategy allowed solvent selection to be based not only on extraction yield, but also on broader sustainability-related parameters. The analysis identified 1,3-propanediol as a suitable bio-based alternative, balancing extraction efficiency, low volatility, and potential application in ready-to-use extracts. High-intensity ultrasound-assisted extraction was subsequently optimized using a central composite rotatable design, considering water content and ultrasound intensity as independent variables. The optimal condition was 1,3-propanediol with 30% water (v/v) and 100% ultrasound intensity until reaching 60 °C. Under this condition, the recoveries were 10.69 ± 0.36 mg g⁻1 theobromine, 0.89 ± 0.01 mg g⁻1 caffeine, 2.08 ± 0.10 mg g⁻1 epicatechin, and 2.42 ± 0.04 mg g⁻1 procyanidin B2. The addition of water likely improved solvent viscosity, acoustic transmission, and mass transfer, contributing to enhanced extraction performance. The optimized system required less extraction time and energy than water and ethanol with 20% water (v/v), retained extraction capacity after reuse, and achieved an indirect extraction yield of 37.0 ± 2.1%. Moreover, solvent reuse increased the cumulative concentration of target compounds, suggesting potential for obtaining more concentrated CBS extracts with reduced solvent demand. Overall, the integration of computational screening, multicriteria decision-making, and ultrasound intensification provided an efficient and sustainable route for CBS valorization, supporting the development of greener processes for agro-industrial by-products.
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