The starvation process of a high-rate partial nitrification system during 30 days and its controlled recovery were studied in an activated sludge pilot plant. Four ammonium-starved reactors under anoxic, aerobic and two different alternating aerobic/anoxic conditions were evaluated. The highest and the lowest decay rates of ammonia oxidizing bacteria (AOB) were obtained under full aerobic (0.24 d(-1)) and full anoxic (0.11 d(-1)) conditions, respectively. The evolution of biomass activity correlated well with the AOB quantification using FISH technique. AOB fractions lower than 1% were measured in the four reactors after 23 days of starvation. The recovery of the system was achieved in only 5 days using a nitrogen loading rate (NLR) control loop, obtaining the same conditions than before the long-term starvation period with a NLR of 1.2 g N L(-1)d(-1) and 98% of nitrite accumulation in the effluent.