Anaerobic Membrane Bioreactor technology has great advantages for treating wastewater, including energy recovery from organic matter. However, when the legislation requires that effluent standards be met in sensitive areas, this treatment cannot remove the nutrients, thus the permeate generated needs post-treatment. Apart from the biological processes, ion exchange is an alternative treatment for this stream since it can remove nutrients and concentrate them for later recovery as fertilizers. In this work, the feasibility of using a natural zeolite (clinoptilolite) for treating NH4 from AnMBR permeate was studied and tests were carried out on the adsorption kinetics of ammonium. Isotherm tests verified that activating natural zeolite to its -Na form improves its performance by 20% and increases qe from 2.37 to 2.86 mg NH4-N/g for a Co of 30 mg NH4-N/L. It was also found that the cations present in the water (especially Ca2+ and Na+) caused a 22% reduction in ammonium adsorption while organic matter was responsible for improving the retained ammonium by 22%. It was also found that the working pH (7.2 ± 0.2) is close to the optimal pH range (6–7) for zeolite performance. The tests on the AnMBR permeate indicate that clinoptilolite is a suitable material since treating this stream can retain up to 7.44 mg NH4-N/g.