High concentrations of nitrogen (N) and phosphorus (P) are reported to originate from uneaten feed and shrimp waste in Central Vietnam. This study aimed to assess the effect of sediment microbial fuel cells (SMFCs) on phosphorus and nitrogen release from different sediments. Dual-chamber SMFCs were set up with drainage sediments collected from intensive (Int) or extensive (Ext) aquaculture pond drainages in Central Vietnam. The experiments were set up under SMFC and no SMFC conditions. Results showed that both sediments showed similar current densities. P and N released from Int-sediment were higher than those from Ext-sediment due to higher organic matter content. In Int-sediment, application of SMFCs reduced P release up to day 20 due to Fe-bound P precipitation, and then P concentration remained stable in the overlying water due to P equilibrium. Besides, SMFCs enhanced ammonium-N (NH4+-N) release from this sediment because of enhancing mineralization. However, in Ext-sediment with low pH and organic matter content, SMFCs did not affect P and N release. In conclusion, SMFC application was effective in suppressing P release from Int-sediment with higher organic matter content.