In this study, Nitrosomonas europaea ATCC 19718 was exposed to silver nanoparticles (AgNPs) of different particle size (7 ± 3 and 40 ± 14 nm) and different coatings (polyvinyl alcohol and adenosine triphosphate disodium). For all different AgNPs used in the study, large aggregates were gradually formed after addition of AgNPs into the media containing N. europaea. The scanning electron microscopy and energy dispersive X-ray spectroscopy of the microstructures suggested that bacterial cells and electrolytes had significant effects on AgNP aggregation. Size- and coating-dependent inhibition of ammonia oxidation by AgNPs was observed, and our analysis suggested that the inhibition was not only due to the released dissolved silver, but also the dispersity of AgNPs in the culture media. Electron microscopy images showed AgNPs could cause the damage of cell wall of N. europaea and make the nucleoids disintegrated and condensed next to cell membrane. Surface-enhanced Raman scattering signals also implied the damage of cell membrane caused by AgNPs. Further protein expression analysis revealed that AgNPs would inhibit important protein functions, including biosynthesis, gene expression, energy production and nitrification to further cause toxicity to N. europaea. Our findings explain the susceptibility of N. europaea to inhibition by AgNPs and the possible interaction between each other. Future research is needed to characterize these effects in more complex cultures and media such as activated sludge and wastewater.