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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.
Common Causes of the Ammonia Smell in Urine. 1  Diet-A person's diet may contribute to the ammonia smell in urine. 2  For example, diets rich in foods that contain nitrogen, such as proteins and leafy greens, may cause the ammonia smell in urine.