In this study, a lab-scale CANON bioreactor was operated for 260days, decreasing operational temperature from 35°C to 15°C and from 466 to 100mg-N L-1 ammonium. This was done in order to check the feasibility of the acclimation of CANON biomass treating anaerobic digestion supernatant to B-stage influent wastewater operational conditions. Results showed that decrease in temperature posed an impact over the performance of the CANON bioreactor as well as over its bacterial assemblage. Nitrogen removal efficiency showed a moderate decrease when the system was acclimated from 35°C to 25°C, but it decreased dramatically in the acclimation from 25°C to 15°C. The decrease in temperature and influent ammonium concentration posed an impact over the bacterial community structure of the system. Ammonium oxidizing bacteria changed from Nitrosomonas, Nitrosospira or Nitrosovibrio genera at high temperature and influent ammonium to Prosthecobacter at low temperature and low ammonium. As well, dominant anammox bacteria genus changed from Candidatus Brocadia to Candidatus Anammoxoglobus during acclimation. Proliferation of nitrite oxidizing bacteria only occurred under low temperature and influent ammonium conditions with growth of Rhodanobacter genus.