Spent sulfite liquor, a side-stream from the pulp and paper industry, is an abundantly available carbon source for bio-based platform chemicals. The biotechnological valorization of side streams in biorefineries is hampered by the inability of many microorganisms to metabolize and deal with aldonic acids. Based on the principles of Green Chemistry, the electrochemical reduction of aldonic acids into the corresponding biomass sugars appears as a prospective process for the conversion of these acids into fermentable carbohydrates. In our paper, the investigation of electrochemical reduction of gluconic and xylonic acids into glucose and xylose, respectively, is presented. The proposed mechanism on a gold-coated silver electrode was determined via ReaxFF molecular dynamics simulations and quantum chemistry calculations. Model solutions with an aldonic acid concentration of 2.5 wt % were used for the experiments. Compared to a two-electrode compartment cell, the amounts of glucose and xylose produced in the undivided cell were more than 4 and 5.5 times higher, respectively. The electrode surface was analyzed by scanning electron microscopy, energy-dispersive X-ray spectroscopy, and X-ray photoelectron spectroscopy. Despite the relatively low conversion rate, our results show that electrochemical reduction of aldonic acids into their corresponding aldoses in model solutions is possible, which represents an important step toward side-stream valorization.