Display omitted •The performance of partial nitritation/anammox process of 15 °C was investigated.•Anammox activity suggested to be the main limitation for the nitrogen removal.•Denitratation process occurred with limited influent organic matter condition.•The main functional bacteria were from genus Nitrosomonas and genus Kuenenia.•PNA, denitratation, and the COD oxidization simultaneously occurred. At ambient temperature condition, the one-stage partial nitritation/anammox (PNA) process has been successfully adopted to treat the filtrate from the mainstream anaerobic membrane bioreactor (AnMBR). However, there is no investigation of the performance of this process at low-temperature condition. In this study, the nitrogen removal performance of a pilot-scale PNA reactor at the temperature of 15 °C for treating the filtrate of a mainstream AnMBR was investigated. The nitrogen removal rate of 0.09 kg/m3/d and the nitrogen removal efficiency of 37.6% were achieved. The anammox reaction was the rate-limiting step of the nitrogen removal. Nitrogen removal was attributed in part to denitrification activity. The microbial community analysis confirmed that the main functional bacteria comprised of genus Nitrosomonas and genus Kuenenia. In sum, this research demonstrated the applicability of PNA process for mainstream AnMBR filtrate treatment to some extent and enriched the related knowledge.