Melanoidins are heterogeneous polymers with a high molecular weight and brown color formed during the Maillard reaction by the combination of sugars and amino acids at high temperatures with the potential to inhibit the microbial activity in bioprocesses. This study assessed the impacts of melanoidins on the kinetic of substrate conversion and production of organic acids via dark fermentation using microbial consortia as inoculum. The investigations were carried out in fed-batch reactors using synthetic melanoidins following glucose-to-melanoidin ratios (G/M; g-glucose g−1 melanoidins) of 0.50, 1.50, 1.62, 1.67, and 5.00, also considering a melanoidin-free control reactor. The results showed that melanoidins negatively impacted the kinetics of glucose fermentation by decreasing the first-order decay constant (k1): when dosing equivalent initial concentrations of glucose (ca. 3 g L−1), the absence of melanoidins led to a k1 of 0.62 d−1, whilst dosing 2 g L−1 (G/M = 1.5) and 6.0 g L−1 (G/M = 0.5) of melanoidins produced k1 values of 0.37 d−1 and 0.27 d−1, respectively. The production of butyric and acetic acids was also negatively impacted by melanoidins, whilst the lactic activity was not impaired by the presence of these compounds. Lactate production reached ca. 1000 mg L−1 in G/M = 1.67, whilst no lactate was detected in the control reactor. The presence of melanoidins was demonstrated to be a selective metabolic driver, decreasing the microbial diversity compared to the control reactor and favoring the growth of Lactobacillus. These results highlight the importance of further understanding the impacts of melanoidins on melanoidin-rich organic wastewater bioconversion, such as sugarcane vinasse, which are abundantly available in biorefineries.