Excessive phosphorus can cause eutrophication in water bodies and needs to be reduced in most wastewaters before discharge to receiving waters. The enhanced biological phosphorus removal (EBPR) process has been shown to be an economical and environmentally compatible method for reducing phosphorus from wastewaters. The experiment has been performed in order to investigate the effect of using effective microorganisms (EM) as an application of Enhanced Biological Phosphorous Removal (EBPR) in modified contact stabilization activated sludge system by using contact tank as a phosphorus uptake zone and using thickener tank as a phosphorus release zone. The study involved the construction of a pilot plant which was setup in the Quhafa Wastewater Treatment Plant (WWTP), Al Fayoum, Egypt. Then the uptake and release of total phosphorus were determined through two batch tests using sludge samples from thickener and stabilization tanks. Results showed the removal efficiencies of Chemical Oxygen Demand (COD), Biological Oxygen Demand (BOD5) and total phosphorus (TP) of this pilot plant were 93%, 93% and 90%, respectively. On the other hand the results of batch tests showed that the reason for high ability of phosphorus removal by this pilot plant is related to the high performance of microorganisms for phosphorus accumulation. Finally providing activated EM to the anaerobic zone was to improve fermentation by achieving the enhancement of the performance of phosphorus accumulating organisms (PAOs) and then increase phosphorous release resulting in the decrease of the average effluent phosphorus concentration.