The objective of this study was to achieve better efficiency of phosphorus removal in an enhanced biological phosphorus removal process by upgrading the system with different amounts of natural zeolite addition. The system performance for synthetic wastewater containing different carbon sources applied at different initial concentrations of phosphorus, as well as for municipal wastewater, was investigated. Natural zeolite addition in the aerobic phase of the anaerobic/aerobic bioaugmented activated sludge system contributed to a significant improvement of phosphorus removal in systems with synthetic wastewater and fresh municipal wastewater. Improvement of phosphorus removal with regard to the control reactors was higher with the addition of 15 than with 5 g/L of natural zeolite. In reactors with natural zeolite addition with regard to the control reactors significantly decreased chemical oxygen demand, ammonium and nitrate, while higher increment and better-activated sludge settling were achieved, without changes in the pH-values of the medium. It was shown that the natural zeolite particles are suitable support material for the phosphate-accumulating bacteria Acinetobacter calcoaceticus (DSM 1532), which were adsorbed on the particle surface, resulting in increased biological activity of the system. The process of phosphorus removal in a system with bioaugmented activated sludge and natural zeolite addition consisted of: metabolic activity of activated sludge, phosphorus uptake by phosphate-accumulating bacteria adsorbed on the natural zeolite particles and suspended in solution, and phosphorus adsorption on the natural zeolite particles.