Diclofenac, ibuprofen, and carbamazepine are frequently detected in the environment, where they pose a threat to organisms and ecosystems. We developed anaerobic–aerobic coupled upflow bioelectrochemical reactors (AO-UBERs) with different voltages, hydraulic retention times (HRTs), and types of electrode conversion, and evaluated the ability of the AO-UBERs to remove the three pharmaceuticals. This study showed that when a voltage of 0.6 V was applied, the removal rate of ibuprofen was slightly higher in the system with aerobic cathodic and anaerobic anodic chambers (60.2 ± 11.0%) with HRT of 48 h than in the control systems, and the removal efficiency reached stability faster. Diclofenac removal was 100% in the 1.2 V system with aerobic anodic and anaerobic cathodic chambers, which was greater than in the control system (65.5 ± 2.0%). The contribution of the aerobic cathodic–anodic chambers to the removal of ibuprofen and diclofenac was higher than that of the anaerobic cathodic–anodic chambers. Electrical stimulation barely facilitated the attenuation of carbamazepine. Furthermore, biodegradation-related species (Methyloversatilis, SM1A02, Sporomusa, and Terrimicrobium) were enriched in the AO-UBERs, enhancing pharmaceutical removal. The current study sheds fresh light on the interactions of bacterial populations with the removal of pharmaceuticals in a coupled system.