Unusual or foul-smelling urine is a common problem for people on a low-carb diet. Diets like the Atkins Diet, the South Beach Diet and the ketogenic diet can cause stinky urine in several different ways.

How High Protein Diets Cause Stinky Urine
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Eating a diet high in protein puts your liver to work. As your liver processes the extra protein you've taken in, it produces ammonia as a by-product. Since ammonia is toxic, your liver converts it to urea. Then your kidneys send it out of your body through your urine. In high enough concentrations, you may notice the unpleasant smell of ammonia in your urine. How noticeable the smell is depends on how concentrated your urine is and how much protein you've been eating.
Low Carb Diets and Stinky Urine
If ammonia levels in your urine are high enough that you can easily smell them, your body is likely also expelling ammonia through your breath and sweat. This could put you in the unfortunate position of battling stinky urine, body odor and bad breath all at once.
High Protein Diets Are Often High In Sulfur

Another reason low-carb diets can cause stinky urine is that many foods high in protein also contain high levels of sulfur. Sulfuric substances are known to cause smelly urine. Red meat, poultry, eggs, fish and nuts are all high in sulfur.
In addition, many of the vegetables that people on a low-carb diet might eat are high in sulfur. Examples include asparagus, broccoli, green beans and peas. Large amounts of sulfur in your diet will not only cause smelly urine, but may cause bad breath and body odor as well.
Increased Ketones In Urine Makes It Smell Bad

One of the biggest reasons high-protein/low-carb diets can cause stinky urine is that they make your body go into ketosis. Ketosis is when your body is using fat for fuel instead of sugar. In most low-carb diets, ketosis is the goal because it is believed to speed up weight loss.

When your body is in ketosis, more ketones (substances resulting from your body burning fat) will be excreted in your urine. This can cause your urine to have a sweet or fruity smell, a smell like rotten fruit or a smell similar to nail polish remover. The type of ketone causing the smell is usually acetone.

It can create quite a dilemma when you have purposely put your body in a state of ketosis to burn fat, but now have foul-smelling urine. After so much work, you may be reluctant to adjust your diet just as you’ve started achieving your goals. On the other hand, no one wants foul-smelling urine.
How To Get Rid of Stinky Urine Caused By High Protein/Low Carb Diets

1. Drink plenty of water. Your body is trying to expel the substances causing your smelly urine. It cannot do that effectively if you are dehydrated. Give your body the water it needs to do its job.

2. Breathe deeply. Your body's main method of eliminating some of the substances that cause stinky urine is through the breath. Acetone and ammonia in particular tend to be released when you exhale. Increasing ventilation gives the body more opportunities to get rid of the substances causing smelly urine, sweat and breath. Just don’t hyperventilate!

3. Increase your carb intake. Eating more carbohydrates will help get rid of stinky urine if it’s caused by a high-protein diet. The problem is that it will do so by bringing your body out of ketosis.

4. Take Urifresh. It neutralizes foul odors in urine caused by high protein, low-carb diets and many other causes. You can buy it on Amazon.com.
Related:

​Causes of Smelly Urine Related to Ketones

Yeast Infections and Stinky Urine

Asparagus and Other Foods that Make Your Pee Smell Bad