Technological advancements in the past few decades have made it possible to manufacture nanomaterials at a large scale, and engineered nanoparticles (ENPs) are increasingly found in consumer products, such as cosmetics, sports products, and LED displays. A large amount of these ENPs end up in wastewater and potentially impact the performance of wastewater treatment plants (WWTPs). One important function of the WWTP is nitrification, which is carried out by the actions of two groups of bacteria, ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). Since most ENPs are found to have or are designed to have antimicrobial activities, it is a legitimate concern that ENPs entering WWTPs may have negative impacts on nitrification. In this paper, the effects of ENPs on nitrification are discussed, focusing mainly on autotrophic nitrification by AOBs and NOBs. This review also covers ENP effects on anaerobic ammonium oxidation (anammox). Generally, nitrifiers in pure and mixed cultures can be inhibited by a variety of ENPs, but stress response mechanisms may attenuate toxicity. Long-term studies demonstrated that a wide range of NPs could cause severe deterioration of AOBs and/or NOBs when the influent concentration exceeded an inhibition threshold. Proposed mechanisms include the generation of reactive oxygen species, dissolved metals, physical disruption of cell membranes, bacterial engulfment, and intracellular accumulation of ENPs. Future research needs are also discussed.