This research sheds light on the gap in knowledge concerning the effect of temperature shock on nitrifiers. This phenomenon was analysed in context of mainstream bioaugmentation with nitrifiers cultivated in a sidestream partial nitritation process, which was recently experimentally confirmed to be beneficial in municipal wastewater treatment plants. In this study, using respirometric activity measurements and a simple mathematical model of nitritation, it has been proven that fluctuations in nitrifier concentration in long term tests affect the value of the estimated temperature correction coefficient (θ). Furthermore, this leads to underestimation of its value and thus, results in inaccurate prediction of the scale of the temperature shock effect. During the first days following the shock occurrence, the estimated process rate using the new approach was equal to only 64.1 ± 9.7% of the value calculated using previously preferred methods. Moreover, faster biomass acclimatisation to lower temperature in the following days was observed. These observations clearly indicate the need for change in the current approach and confirm the validity of the proposed improvements. It can be assumed, that the presented insights concerning the method of temperature effect assessment are transferrable to other microbial communities involved in biological wastewater treatment processes.