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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.
These are some of the few most common reasons why your urine might smell like ammonia: 1  High-protein Foods Consumption. Eating foods rich in protein can cause this smell, especially if you eat a lot of them. 2  Dehydration. If you don't have enough water in your body, your urine becomes very concentrated. 3  Holding Urine for Too Long.