BACKGROUND: Coffee pulp (CP), cocoa husk (CH), and pod husk (CPH) are the main agro-residues from coffee and cocoa industries. They are sources of useful biomolecules, such as phenolic compounds, fibers, and alkaloids, among others. In this study, different compositions of deep eutectic solvents (DES) were investigated as a green and sustainable extraction media, with respect to their extraction capacity. The extraction yields were evaluated using heat stirring-assisted extraction (HSE) or ultrasound-probe assisted extraction (UPAE). RESULTS: The results showed an important effect of the DES composition. Choline chloride (ChCl) based-DES were the most effective, specifically lactic acid:ChCl (2:1 mol ratio), and the extraction capacity of DES was higher with UPAE (3 min/constant duty cycle (200¿W)), in comparison with HSE (1 h/30¿min). Chlorogenic acid, caffeine, and theobromine were identified as the main bioactive compounds. Interestingly, under specific conditions, DES allowed the formation of a molecule, identified as furfural by ultrahigh-performance liquid chromatography mass spectrometry (UPLC-MS), which could not be obtained using conventional extraction solvent (ethanol 70% v/v). CONCLUSION: DES showed a sustainability and high extraction capacity of biomolecules. In addition, their use as extraction solvents could lead to the formation and production of valuable building block molecules from plant biomass. © 2019 Society of Chemical Industry.