The objective of this study was to define an automatic control loop for the start-up of a high-strength nitrification system to achieve a rich nitrifying biomass from a poor nitrifying sludge by means of simulation tools. The used model considered the nitrification as a two-step model with substrate and non-competitive inhibitions. Two control strategies (on-off controller and proportional-integral (PI) controller) were designed, simulated and compared. The measured variable in the control loops was the sum of ammonium and nitrite concentrations in the effluent and the manipulated variable was the inflow. The objective in the optimisation of both controllers was to increase the inflow of the system as fast as possible without exceeding the maximum ammonium and nitrite concentrations allowed in the effluent. The optimised controllers parameters were used to simulate a 40 days start-up. The results obtained with both strategies were similar, although, the best strategy was the PI controller since it was less oscillatory and the biomass growth was slightly faster.