The hydrogenation/hydrogenolysis of 5-hydroxymethylfurfural (HMF) has been carried out either under single (aqueous) phase or batch multiphase (MP) conditions using mutually immiscible aqueous/hydrocarbon phases, 5 % Ru/C as a catalyst, and both with and without the use of trioctylmethyl phosphonium bis-(trifluoro methane) sulfonimide ([P8881][NTf2]) as an ionic liquid (IL). Alternatively, the hydrogenation of HMF was explored in the continuous-flow (CF) mode with the same catalyst. By changing reaction parameters, experiments were optimized towards the formation of three products: 2,5-bis(hydroxy methyl)furan (BHMF), 2,5-bis(hydroxymethyl)tetrahydrofuran (BHMTHF), and 1-hydroxyhexane-2,5-dione (HHD), which were obtained in up to 92, 90, and 99 % selectivity, respectively, at quantitative conversion. In particular, the single (aqueous) phase reaction of HMF (0.2 m) carried out for 18 h at 60 °C under 30 bar of H2, allowed the exclusive synthesis of BHMF from the partial (carbonyl) hydrogenation of HMF, while the MP reaction run at a higher T and p (100 °C and 50 bar) proved excellent to achieve only HHD derived from a sequence of hydrogenation/hydrogenolysis. It is worth noting that under MP conditions, the catalyst was perfectly segregated in the IL, where it could be recycled without any leaching in the aqueous/hydrocarbon phases. Finally, the hydrogenation of HMF was explored in a H-Cube® flow reactor in the presence of different solvents, such as ethyl acetate, tetrahydrofuran, and ethanol. At 100 °C, 50 bar H2, and a flow rate of 0.1 mL min−1, the process was optimized towards the formation of the full hydrogenation product BHMTHF. Ethyl acetate proved the best solvent. © 2022 The Authors. ChemSusChem published by Wiley-VCH GmbH.