Process of partial nitritation-anammox for mainstream wastewater at low temperature was run in a pilot scale moving bed biofilm reactor (MBBR) system for about 300 days. The biofilm history in the reactor was about 3 years of growth at low temperature (down to 10 °C). The goal of the studies presented in this paper was to achieve effective partial nitritation-anammox process. Influence of nitrogen loading rate, hydraulic retention time, aeration strategy (continuous versus intermittent) and sludge recirculation (integrated fixed-film activated sludge (IFAS) mode) on deammonification process' efficiency and microbial activity in the examined system was tested. It was found that the sole intermittent aeration strategy is not a sufficient method for successful suppression of nitrite oxidizing bacteria in MBBR. The best performance of the process was achieved in IFAS mode. The highest recorded capacity of ammonia oxidizing bacteria and anammox bacteria in biofilm was 1.4 gN/m2d and 0.5 gN/m2d, respectively, reaching 51% in nitrogen removal efficiency.