Bioaugmentation with nitrifiers was studied using two pilot-scale membrane bioreactors, with the purpose of assessing the suitability of state-of-the-art activated sludge models (ASMs) in predicting the efficiency of bioaugmentation as a function of operating conditions. It was demonstrated that the temperature difference between seeding and seeded reactors (ΔT) affects bioaugmentation efficiency. Experimental data were accurately predicted when ΔT was within a range of up to 10 °C at the higher range, and when the temperature was significantly lower in the seeded reactor compared to the seeding one, standard ASMs overestimated the efficiency of bioaugmentation. A modified ASM, capable of accurately representing the behavior of seeded nitrifying biomass in the presence of high ΔT, would require the inclusion of the effect of temperature time gradients on nitrifiers. A simple linear correlation between ΔT and the Arrhenius coefficient was proposed as a preliminary step.