The biocide Free Nitrous acid (FNA) is known to have strong inhibitory and biocidal effects in parts per billion (ppb) and parts per million (ppm) levels. Consequently FNA has been applied in a number of engineered systems to control microbial growth such as reducing microbial induced sewer corrosion and foul odour caused by sulphate reducing bacteria in sewer pipes. Most micro-organisms have very low tolerance to FNA, however among nitrifiers found in the activated sludge process of wastewater treatment plants, ammonia oxidising bacteria (AOB) rather than nitrite oxidising bacteria (NOB) have higher tolerance to FNA, this despite NOB having more pathways available for detoxification. To date there is little understanding of the biocidal and inhibitory mechanisms of FNA, and reasons for the difference in tolerance among nitrifiers is unknown. Herein we investigate the reasons for this atypical behaviour in AOB using a quantitative SWATH-MS meta-proteomics method in an enriched activated sludge system. On investigation we found that FNA tolerance in AOB is primarily due to the up regulation of the oxidative stress enzymes such as peroxidases and reductases that remove reactive nitrogen species in response to oxidative stress caused by FNA. Enzymes involved in ATP production for AOB such as ammonia mono-oxygenase (amo) and hydroxylamine oxidoreductase (hao) were up-regulated suggesting that ATP could be used for energy dependent detoxification mechanisms such as the conversion of nitrite to ammonia as evidenced from the quantitative meta-proteomics. This multi-‘omic’ approach provides the first detailed quantitative meta-proteomic approach to study the antimicrobial effect of the biocide Free Nitrous acid on AOB and NOB found in activated sludge.