Pairing the electrocatalytic hydrogenation (ECH) reaction with different anodic reactions holds great promise for producing valuable chemicals driven by renewable energy. Replacing the sluggish water oxidation with a bio-based upgrading reaction can reduce the overall energy cost and allows for the simultaneous generation of high-value products at both electrodes. Herein, we developed a membrane-electrode assembly (MEA)-based electrolysis system for the conversion of 5-(hydroxymethyl)furfural (HMF) to bis(hydroxymethyl)furan (BHMF) and 2,5-furandicarboxylic acid (FDCA). With TEMPO-mediated electrochemical oxidation (ECO) of HMF at the anode, the unique zero-gap configuration enabled a minimal cell voltage of 1.5 V at 10 mA, which was stable during a 24-hour period of continuous electrolysis, resulting in a combined faradaic efficiency (FE) as high as 139% to BHMF and FDCA. High FE was also obtained in a pH-asymmetric mediator-free configuration, in which the ECO was carried out in 0.1 M KOH with an electrodeposited NiFe oxide catalyst and a bipolar membrane. Taking advantage of the low cell resistance of the MEA-based system, we also explored ECH of HMF at high current density (280 mA cm−2), in which a FE of 24% towards BHMF was achieved. The co-generated H2 was supplied into a batch reactor in tandem for the catalytic hydrogenation of furfural or benzaldehyde under ambient conditions, resulting in an additional 7.3% of indirect FE in a single-pass operation.