Bioreduction can facilitate oxyanions removal from wastewater. However, simultaneously removing selenate, nitrate and sulfate and recovering high-purity elemental selenium (Se0) from wastewater by a single system is difficult and may lead to carcinogenic selenium monosulfide (SeS) formation. To solve this issue, a two-stage biological fluidized bed (FBR) process with ethanol dosing based on oxidation-reduction potential (ORP) feedback control was developed in this study. FBR1 performance was first evaluated at various ORP setpoints (between −520 and −360 mV vs. Ag/AgCl) and elevated sulfate concentration. Subsequently, ethanol-fed FBR2 was used to reduce sulfate from FBR1 effluent, followed by an aerated sulfide oxidation reactor (SOR). At − 520 mV ≤ ORPs ≤ − 480 mV, FBR1 removed 100 ± 0.1% nitrate and 99.7 ± 0.3% selenate without sulfate reduction. At ORPs ≥ − 440 mV, selenate reduction was incomplete, whereas nitrate removal remained stable. Se0 recovery efficiency from FBR1 effluent was 37.5% with 71% Se purity. FBR2 converted 86% of the remaining sulfate in FBR1 effluent to hydrogen sulfide, but the over-oxidation of dissolved sulfide in SOR decreased the overall sulfate removal efficiency to ~46.3%. Overall, the two-stage FBR process with ORP feedback dosing of ethanol was effective for sequentially removing selenate, nitrate and sulfate and recovering Se0 from wastewater.