This study evaluated the influence of clinoptilolite on the performance of activated sludge system shocked by high concentration of ammonium. The ammonium and chemical oxygen demand (COD) removal from the experimental reactor containing clinoptilolite and from the clinoptilolite-free control reactor was determined. The ammonium and COD removal was approximately 8 and 20% higher in the experimental reactor than in the control reactor, respectively. The removal increased with an increase in clinoptilolite concentration over the tested range up to 50 mg L^-1. The presence of clinoptilolite resulted in the sludge flocs being more compacted with smoother surfaces and edges. Molecular biological analysis revealed that clinoptilolite increased the DNA diversity, richness, and evenness of sludge microbes. The enhanced-performance activated sludge previously treated with clinoptilolite was less influenced by the shock of ammonium than non-treated sludge in terms of the ammonium and COD removal. These results suggest that clinoptilolite enhanced the performance of activated sludge system in the removal of ammonium and COD. Amendment of activated sludge with natural zeolites may thus improve the efficiency of wastewater treatment.