Municipal wastewater in temperate climates is characterized by seasonal temperature changes. Temperature is a determining factor for biological processes, but the impact of gradually decreasing temperature on aerobic granular sludge (AGS) has been largely unexplored. In this study, the influence of decreasing temperature from 20 °C to 6 °C on AGS was investigated at rates of 0.5 and 1 °C per week. Temperature was a major driver for microbial community change, where the community response could be divided into three main subclusters. Strains within the guilds of ammonium- and nitrite-oxidising bacteria (AOB and NOB) as well as polyphosphate- and glycogen-accumulating organisms (PAOs and GAOs) grouped in different subclusters, indicating variable responses among and between the guilds. The phosphorous removal rate was sufficient for complete removal at all temperatures, presumably due to functional redundancy within the PAOs. The nitrification rate was, however, seriously impaired below 13 °C, despite diversity within AOB and NOB.