Wastewater quality and malodors in a second generation implementation of environmentally superior technology (EST) were monitored over three cycles of pig (Sus scrofa) production and 15 mo. The wastewater treatment system consisted of three modules: solids separation, biological N removal, and P recovery/wastewater disinfection. While approximately more than 90% of the wastewater suspended solids were removed in the first stage of treatment, little reduction in malodorous compounds occurred, indicating that malodors largely remained with the liquid waste stream. The greatest improvements in wastewater quality occurred in the N treatment module where ammonium was removed through nitrification/denitrification processes: there was more than 99% reduction in aromatic malodorous compounds (e.g., p‐cresol, skatole) and almost 90% reduction in volatile fatty acids (e.g., propanoate and butanoate) in N module effluent as compared to raw flushed manure. The system performed consistently well in wastewater odor removal, even during the first cycle of livestock production when system performance was being optimized. These findings showed that the combination of the processes of solids removal and biological N treatment into a practical treatment system can be very effective in reducing malodors from livestock wastewater.