Experiencing unusual smelling urine or even foul smelling urine is a common issue for those on low carb diets. Diets like the Atkins Diet, South Beach Diet, Paleo Diet and the Ketogenic Diet can cause smelly urine for several different reasons.

High Protein Diets Cause Stinky Urine
​
Low carb diets are usually high in protein. Consuming all that extra protein makes your liver work harder, and ammonia is a by-product of that. Ammonia is toxic to the body, so the liver converts it to urea. It is then expelled from the body in urine. If you have very high concentrations of ammonia, you might even be able to smell it in your urine.
If ammonia levels in your urine are high enough that you can easily smell them, your body is probably also releasing ammonia through your breath and sweat as well. This could put you in the unfortunate position of battling stinky urine, body odor and bad breath all at once.
Low Carb Diets and Stinky Urine
High Protein Diets Are Often High In Sulfur

Lots of foods that are high in protein also happen to be high in sulfur, which is known to cause stinky urine. Red meat, poultry, eggs, fish and nuts all have high sulfur content.
On top of that, many vegetables low carb diets allow contain high levels of sufur. Asparagus, broccoli, green beans and peas, for example, are all offenders. As mentioned above, if your diet has high levels of sulfur, it may cause not only stinky pee, but bad breath and body odor.
Higher Ketone Levels In Urine Make It Smell Bad

High protein/low carb diets can cause your body to go into ketosis, which is another main reason these types of diets can cause stinky pee. Ketosis is when your body is using fat as fuel instead of sugar. In many low carb diets, ketosis is the goal because it is believed to encourage weight loss.
When your body burns fat, it produces more ketones. That can make your pee have a sweet or fruity smell or make it smell like acetone/nail polish remover.
The problem that most people on low carb diets face is that being in ketosis is a necessary part of their diet. If ketosis comes with foul smelling urine, it’s hard to change your diet, knowing it might affect your weight loss goals. On the other hand, nobody wants stinky urine!