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1 If the liver is unable to break down the ammonia it is excreted in the urine.  Other diseases - Other common causes of the ammonia smell in urine are diabetes, metabolic disorders, sexually transmitted diseases, medications, vitamins, and nutritional supplements.
1 Alternatively, if your diet is the cause of the ammonia smell in your urine then dietary changes may be necessary to treat the condition. 2  It may take a few days for changes to your diet to get rid of the ammonia smell in urine. For example, diets rich in foods that contain nitrogen, such as proteins and leafy greens, may cause the ammonia smell in urine. 2  When large amounts of nitrogen-rich foods are ingested the excess nitrogen is released in the urine, thus contributing to its ammonia smell.