The start-up of a biological nitrifying system to treat high-strength ammonium wastewater must be done carefully to avoid ammonium or nitrite build-up and subsequent system destabilization due to inhibition. This article shows the start-up with automatic control of a complete nitrification system in a pilot plant. Firstly, a manual start-up was performed with manual increases in the nitrogen-loading rate (NLR). Secondly, two control strategies for controlled start-up based on oxygen uptake rate (OUR) measurements were successfully implemented and compared in the pilot plant. The successful enrichment of the microbial community in nitrifying microorganisms was corroborated with fluorescence in situ hybridization (FISH) quantification. Finally, the results of both controlled start-up strategies were simulated with a mathematical model considering the nitrification as a two-step process. © 2008 Elsevier B.V. All rights reserved.