Soybean molasses (SM), a sugar-rich by-product obtained from manufacturing soy protein concentrate, was used as a new and low-cost substrate to produce gluconic acid (GA) by Aspergillus niger. SM with total sugar concentrations of 46% and 52% (w/w) were tested to assess the effect of SM composition, sugar concentration, and sugar profile on GA synthesis in batch cultures in a stirred-tank bioreactor.GA productivity improved as the total sugar concentration increased, whereas yield was unaffected. Agitation rate increase positively affected yield and productivity in SM medium with the highest sugar concentration. Under these conditions, the highest GA titer (79 g·L-1) was obtained. Oxalic acid and fructose syrup were other added-value compounds found from the submerged fermentation of SM. This work proved the potential of A. niger in the bioconversion of SM with different compositions into GA, providing a novel strategy for low-cost and eco-friendly GA production.