Nitrification can be difficult to maintain at wastewater treatment plants (WWTPs) during cold periods resulting in disrupted nitrogen removal. The aim of this study was to relate nitrification process performance to abundance and composition of the ammonia oxidizer communities in two closely located municipal WWTPs in Sweden during an eight month period covering seasonal changes and low temperature conditions. Both facilities showed lower NH4+-N removal efficiency and nitrification rates as temperature decreased. However, one of the plants had a more stable nitrification rate and higher ammonia removal efficiency throughout the entire period. The differences in performance was related to a shift in the composition of the bacterial ammonia oxidizing community from a Nitrosomonas oligotropha-dominated community to a mixed community including also Nitrosomonas ureae-like ammonia oxidizers. This was likely a response to differences in NH4+-N and organic loading.