This work assessed the impact of microaeration and the redox mediator anthraquinone-2,6-disulfonate (AQDS) on both azo dye reduction and by-products degradation (aromatic amines) in a mesophilic reactor. The experiment was carried out in an up-flow anaerobic sludge blanket (UASB) reactor with 3.2 L of working volume and hydraulic retention time (HRT) of 24 h. The synthetic effluent contained 50 mg L À1 of the dye Reactive Red 2 (RR2). The reactor was initially operated under anaerobic conditions and, subsequently, was microaerated with atmospheric air (1 mL min À1 ) and then supplemented with the redox mediator (AQDS) at a concentration of 25 μM. The microaeration effect on dye reduction and by-products formed was not evident. However, AQDS considerably enhanced RR2 reduction, and its regeneration was not affected by the presence of oxygen. It seems that the cleavage of the double bond between nitrogen groups is a much easier way to start the attack of the azo dye, and it is independent of the presence of oxygen. Thus, the introduction of hydroxyl groups into the aromatic ring was not playing a role in the color removal process. In terms of ecological parameters, the ecological niches were maintained, and the distribution of species increased, despite the majority being generalists, i.e., not specialized in dye degradation. Furthermore, anaerobic species are dominant over facultative species, which explains why there was no population diversity recovery after the microaeration started.