Microbial fuel cells (MFCs) provide a cost-effective method for treating swine wastewater treatment and simultaneously producing electricity, yet they need to be combined with other wastewater treatment processes to improve the effluent water quality. In this paper, we constructed single-chamber air-cathode MFCs with a compact configuration for nitrogen and COD removal and high electricity production and combined them with a low-cost flocculation process to discharge higher quality wastewater. We show that MFCs could remove ammonia at a rate of 269.2 ± 0.5 g m-3 d-1 (99.1± 0.1% ammonia removal efficiency) with a maximum power density of 37.5 W m-3 and 21.6% of coulombic efficiency at a 40:60 ratio of raw swine wastewater to denitrification effluent of swine wastewater. Up to 82.5 ± 0.5% COD could be removed with MFCs, from 2735 ± 15 mg L-1 to 480 ± 15 mg L-1, and flocculation further reduced levels to 90 ± 1 mg L-1 for a 96.6 ± 0.2% overall COD removal efficiency of the combination technology. Cost analysis of the combined MFC and flocculation process showed a net economic benefit of $ 0.026 m-3. In summary, this novel combination wastewater treatment method provides an effective way to treat swine wastewater to low pollutant levels in the effluent at low cost (a net gain).