This study presents a novel strategy for cultivating anammox bacteria from tropical environments using a filter bioreactor (FtBR). Two bioreactors were inoculated with sediment sludge from an Indonesian lake and operated at different temperatures: tropical ambient (22–28 °C) in Reactor 1 and 35 °C in Reactor 2. After 106 days, Reactor 1 developed a red carmine anammox biofilm, while Reactor 2 remained similar to its initial state. Reactor 1 achieved a higher and more stable nitrogen removal rate (0.27 kg-N/m3·d) compared with Reactor 2 (0.21 kg-N/m3·d), indicating a 28.6% greater efficiency. The operational temperature significantly influenced the diversity and abundance of anammox bacteria. Candidatus Brocadia caroliensis (6.20%) was detected in Reactor 1, whereas Candidatus Anammoxoglobus propionicus (7.64%) and Candidatus Brocadia sinica (1.77%) were found only in Reactor 2. Additionally, Candidatus Brocadia fulgida was more abundant in Reactor 1 (20.04%) than in Reactor 2 (6.84%). These findings demonstrate that temperature plays a crucial role in starting the anammox process in FtBRs with a resident inoculum from tropical environments, significantly affecting bacterial growth and nitrogen removal efficiency.