An improved method of controlling a wastewater treatment plant, by identifying a condition and as a result of this apparent condition changing the treatment of the waste water. It especially relates to a method of improving the nutrient removal in wastewater treatment plants. The control method includes a cycle with two phases, a first and a second phase. In the first phase aeration continues until sufficient nitrification is obtained and an uptake of phosphate reaches a defined level based on the current load or capacity situation. Then the second phase continues until sufficient denitrification is obtained and until the storage of intercellular compounds in phosphorus accumulation organisms (PAO) reaches a defined level.