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In this work, a deep eutectic solvent (DES) composed of choline chloride (ChCl) and ethylene glycol (EG) was prepared and applied for the conversion of fructose to 5-hydroxymethylfurfural (HMF), catalyzed by HCl in both laboratory batch reactors and continuous flow microreactors. The effects of reaction temperature, batch time, catalyst loading and molar ratio of ChCl to EG on the fructose conversion and HMF yield were first investigated in the monophasic batch system of ChCl/EG DES. To inhibit HMF-involved side reactions (e.g., its polymerization to humins), methyl isobutyl ketone (MIBK) was used as the extraction agent to form a biphasic system with DES in batch reactors. As a result, the maximum HMF yield could be enhanced at an MIBK to DES volume ratio of 3:1, e.g., increased from 48% in the monophasic DES (with a molar ratio ChCl to EG at 1:3) to 63% in the biphasic system at 80°C and 5 mol% of HCl loading. Based on the optimized results in batch reactors, biphasic experiments were conducted in capillary microreactors under slug flow operation, where a maximum HMF yield of ca. 61% could be obtained in 13 min, which is similar to that in batch under otherwise the same conditions. The slight mass transfer limitation in microreactors was confirmed by performing experiments with microreactors of varying length, and comparing the characteristic mass transfer time and reaction time, indicating further room for improvement. Highlights • The efficient fructose conversion to HMF in deep eutectic solvents was achieved in batch reactors and microreactors. • An HMF yield over 60% could be obtained at a fructose conversion above 90% in both reactors at 80°C within 14 min. • The HMF yield was enhanced from 48% in the monophasic ChCl/EG system to 63% in the DES-MBIK biphasic system in batch. • A slight mass transfer limitation was found in the biphasic slug flow microreactor. Graphical Abstract