Partial nitritation-anammox (PN-A) has gained increasing interest for municipal wastewater treatment in recent years due to its high energy-saving potential. Moving the PN-A technology from side- to mainstream exhibited a set of challenges. Conditions are quite different, with much lower ammonium concentrations and temperatures. Biomass retention becomes highly important due to the even lower growth rates. This study compared two laboratory-scale reactors, a sequencing batch reactor (SBR) and a moving bed biofilm reactor (MBBR), employing realistic seasonal temperature variations over a 1-year period. The results revealed that both systems had to face decreasing ammonium conversion rates and nitrite accumulation at temperatures lower than 12°C. The SBR did not recover from the loss in anammox activity even when the temperature increased again. The MBBR only showed a short nitrite peak and recovered its initial ammonium turnover when the temperature rose back to >15°C. The SBR had higher biomass specific rates, indicating that suspended sludge is less diffusion-limited but also more susceptible to biomass wash-out. However, the MBBR showed the more stable performance also at low temperatures and managed to recover. Ex situ batch activity tests supported reactor operation data by providing additional insight with respect to specific biomass activities.