Moniliella wahieum Y12T (M. wahieum Y12T), a fungal isolated from biodiesel caused serious biodiesel contamination and resulting in biofouling and corrosion, especially during storage. Nanoparticles (NPs) composed of silver, copper, iron, and graphene or their binary mixtures were examined as environmental inhibitors against the fungus Moniliella wahieum Y12T, a biodiesel contaminant. Exposure of M. wahieum Y12T and Escherichia coli (E. coli) to low concentrations of Ag-based nanoparticles (from 0.01 to 0.05 mg mL-1) resulted in excellent growth inhibition. The half-maximal inhibitory concentration (IC50) of M. wahieum Y12T by La₂O₃ NPs was 138 times greater when compared with silver (AgO). The median effective concentration (EC50) of La₂O₃ NPs on E. coli was 379 times more than M. wahieum Y12T. At this same concentration, E. coli was uninhibited after exposure to the NPs. However, a fluorescein diacetate analysis showed the Ag-based NPs (including AgO, AgO-Fe₃O₄ and GO-Cu-AgO) significantly reduced the metabolic activity for both of the compared organisms. Compared with other metal oxide NPs, AgO and AgO-Fe₃O₄ NPs display strong bactericidal effect with higher stability and dispersibility, with the zeta potential of -22.27 mV and poly-dispersity index (PDI) values of 0.36. These results demonstrate the broad-spectrum biological inhibition that occurs with both Ag-based bimetallic and graphene oxide nanoparticles and the combined utilization of Ag-based NPs paves a new way for inhibits the biodegradation of biodiesel.