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This work studies the partition of phenolic compounds, namely caffeic acid, syringic acid, vanillic acid, ferulic acid, and vanillin, in aqueous two-phase systems (ATPSs) formed by acetonitrile and deep eutectic solvents (DESs) based on choline chloride ([Ch]Cl) and carbohydrates (sucrose, d-glucose, d-mannose, arabinose, and d-xylose). The binodal curves built at 25 °C and 0.1 MPa using DES were compared with ATPS composed of [Ch]Cl and the same carbohydrates. The ability to form ATPS depends on the number and kind of hydroxyl groups in DES's hydrogen-bond donor compound (carbohydrates). ATPS based on DES showed biphasic regions larger than the systems based on [Ch]Cl and carbohydrates alone due to the larger hydrophilicity of DES. The ATPS were used to study the partition of the phenolic compounds. For all the systems, the biomolecules preferentially partitioned to the acetonitrile-rich phase (K > 1), and the best recovery in the top phase ranged between 53.36% (caffeic acid) and 90.09% (vanillin). According to the remarkable results, DES-based ATPS can selectively separate ferulic acid and vanillin for the top phase and syringic, caffeic, and vanillic acids for the bottom phase, achieving a selectivity higher than two. [ABSTRACT FROM AUTHOR]