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Are Your Workouts Actually Shrinking Your Muscle? If your workout clothes smell like ammonia after a workout, this could mean that you're burning a lot of protein for fuel. Ammonia is a by-product of protein metabolism. Ammonia is toxic, so the body reverts to the more primitive removal system through sweat. This is not a good thing because burning protein means you may be using your muscle tissue for energy instead of carbohydrates or body fat. The simple cure is to slightly increase the carbohydrate in your diet and increase your intake of water during the day to dilute the ammonia. Read more