The aim of this study is to investigate ammonium removal from a wastewater resulted after homogenization and anaerobic digestion of a mixture of wastes and wastewater from animal processing units and sewage sludge, by using natural zeolite clinoptilolite. Batches as well as closed loop fixed bed system (CLFB) are studied, offering an alternative to conventional fixed bed systems. The experimental results showed that the optimum pH is in the vicinity of 6.48, where the achieved removal in the batch system reached 46%. The CLFB system, under the same experimental conditions and relative flow rate of 2.56 BV h-1, reached a removal of 55%, which is almost 22% higher. In the CLFB the removal of ammonia could be further increased by diluting the initial solution by 1/8, reaching the level of 96%. The achieved zeolite loading, for all studied systems, is between 2.62 and 13 mg g-1. This kind of operation is very useful for relatively high concentration and small volumes of wastewater and in systems that there is no need for continuous flow operation.