ABSTRACT Industrial wastewaters from the cosmetic industry contain high organic strength and mixture of nanoparticles (NPs). Sediment microbial fuel cell (MFC) is an emerging nature-based technology that can treat complex wastewaters. The aim of this study is to understand the effect of a binary mixture of zinc oxide (ZnO) and copper oxide (CuO) NPs (concentration: 1 + 1 and 10 + 10 mg/L) on the organic matter removal, power generation, and biofilm health of sediment MFCs after a long-term operation of 120 days. The high chemical oxygen demand (COD) removal (>95%) observed for all reactors signified the minimal impact of 10 mg/L NP mixture on treatment. The dissolved organic carbon (DOC) removal from the sediment was reduced by 8% due to NPs. NPs also led to 42.2% higher anode extracellular polymeric substances (EPS) and 46.65% lesser cathode EPS generation. The maximum power density of 0.29 mW/m2 was obtained for the 10 mg/L NP reactor, with the average being 23% higher than the no-NP control reactor. This was the first study to explore the effect of the mixture of NPs on the performance of an MFC. The results indicated that sediment MFCs can sustain high mixture concentrations of NPs. Furthermore, variation of parameters can aid in establishing the feasibility of this technology for treating wastewater with NPs.