This paper compares two control strategies for a nitrification process. The objective is to achieve partial nitrification and thus to accumulate nitrite instead of nitrate. To this end, change in temperature setpoint and active control of oxygen and ammonia concentrations are evaluated in the long term. Evaluation is made on the control performances that are obtained, but also – and more importantly – on the microbial diversity. In particular, it is shown that the combined oxygen and ammonia control strategy is more appropriate since shift in the temperature setpoint strongly affects the composition of the microbial ecosystem present in the reactor whereas active control of oxygen and ammonia does not.