Mental Health Plartform.

Why do I have chronic diarrhea on keto?


You have switched to keto for your mental health, and you feel better, but you cannot seem to get your digestion right. You still have loose stools, and it is way past the adaptation phase. What is happening?


At first, there is a diuretic effect as your body sheds extra water it used to need on hand to digest all those carbs you were eating. But that should resolve in a few days. If loose stools are still occurring after a week or so, many people need small amounts of ox bile to help the digestion of fats, or even just digestive enzymes for a few months to help their body out while things are healing and micronutrient insufficiencies are being worked out. The loose stools and diarrhea eventually stop, whether because their own body upregulated what was needed for digestion or because their gut bacteria was sorted out positively. Most people who adopt a ketogenic diet enjoy improved much-improved digestion and a resolution of intestinal issues.

But for some people, particularly those who are eating a version of keto that is primarily animal-based products, or who are even carnivore exclusively, they can have chronic loose stools and not know what could be causing it. They have waited patiently for weeks and up to several months for the loose stools and diarrhea to stop, and it just hasn’t. 

And to make things even more confusing, they notice that if they add back more plants, it can help reduce or stop the loose stools. Usually, when someone has digestive issues, we can see a worsening of symptoms when we add increased plants, often because fiber can irritate a gut that is trying to heal. But for these people, their digestion seems to get better. At least when it comes to loose stools.

But for some people on the ketogenic diet, adding more vegetables seems to help chronic loose stools. So what is going on? Does it mean a ketogenic diet based primarily on animal foods is bad for you? Not at all. Can you add plant fiber back in to stop diarrhea? Yes, but it won’t fix the underlying issue causing it, and it may worsen things in the long run. In this blog post, we will talk about why. 

It’s about bile, but not like you think

If you still have diarrhea after adopting your very low-carbohydrate ketogenic diet for your mental health, the problem may not be that you don’t make enough bile; it could mean that you make a lot. And possibly too much. This condition is called bile-acid malabsorption or bile-acid diarrhea.

What does bile do exactly?

  • You need bile to break down the fats you eat
  • You need bile to absorb fat-soluble nutrients like Vitamin A and K
  • You need bile to detox yourself from waste products, too much of certain hormones, environmental and ingested toxins

Now for some science stuff

Bile acids are made in the liver using cholesterol using an enzyme pathway called CYP7A1. This enzyme pathway creates two bile acids called cholic acid and chenodeoxycholic acid (CDCA). They are then bound with the two amino acids called taurine and glycine. Once this happens, this little mixture is called bile, and it is stored and made ready for your next amazing keto meal.

When you eat that keto meal with all of that wonderful fat, it triggers a hormone called cholecystokinin. This hormone causes your gallbladder to contract, and it squirts the bile out to help you digest your meal.

In the duodenum, bile emulsifiers fats and let them be broken down by enzymes and absorbed. Bile synthesis is expensive for your body to make, and you will try to recycle almost all of the bile acids you make. 

This reabsorption takes place in the lower part of the intestine through transport proteins in the intestinal wall (ASBT). In normal bile function, only a small amount of unrecycled bile makes it into the colon. Bile gets broken down, and parts are reabsorbed again by reentering circulation (enteropathic recycling). The liver takes these used bile acids, mixes them with more of those amino acids, and creates bile acids again for use by the gallbladder.

When you have bile acid diarrhea, you have too much bile, or the bile you are making is not being reabsorbed. So you end up with too much bile in your colon. And colons are not made to have bile in them. Bile is very irritating and toxic to the colon cells. The irritating nature of bile in your colon will cause it to draw water in and trigger diarrhea. Your colon knows it has to get that bile out of there. And it has no consideration for you in the process.

This condition is very common and makes up about 30% of individuals with IBS-D or SIBO. Some people who get this condition often have lost a part of their colon through injury or surgery. It is also seen in Crohn’s disease and is thought to happen because the inflammation of the gut interferes with their ability to make and use transport proteins needed to recycle bile. 

But you don’t need Crohn’s disease or a loss of part of your colon to have this problem, and it can be a malfunction all on its own called Primary Bile Acid Malabsorption. Because their symptoms are not in response to another disease process, their problem is not the reabsorption of bile acids, and it is instead that they make too much bile.

This dysfunction comes from the FXRFGF19 axis. This axis is responsible for the communication that needs to occur to tell your body that it has enough bile acid and can stop making more. 

But sometimes, the functioning in this FXRFGF19 axis is broken, and it creates an excess of bile production in the liver, causing bile acid diarrhea. This means that there is excess bile, not because the body can’t recycle it well, but because the body keeps overproducing it. And this excess bile ends up in the colon, causing loose stools and diarrhea. 

Is the answer more carbs or more vegetables?

So why does this condition improve when you add more vegetables? The fiber that you get in vegetables helps bind the excess bile acids and prevents them from traveling into the colon and causing diarrhea. So adding more vegetables can help, but it won’t fix why FXR is under-activated in the first place. And neither will increasing your dietary carbs. And if you already have a lot of gut inflammation, we don’t want you to add the fiber back necessarily and you definitely don’t want to feed the bad bacteria you are trying to get rid of more carbs. This would not fix the problem. 

So why is FXR not being activated in the first place? What is going wrong?  

How do I fix this?

Below are factors contributing to your potential FXR dysfunction causing too much bile acid production.

Intestinal or Systemic Inflammation and/or Gut Dysbiosis

Intestinal inflammation can reduce the activity of FXR, all by itself. So if we get your FXR working well again, that can help you reduce inflammation, make healthy gut bacteria, heal your gut barrier, and help you absorb fat-soluble vitamins. 

Side note: High Omega-6 oil intakes, like what happens when your use processed industrialized oils (e.g., canola, soybean, vegetable), also messes with the FXR protein and disables this axis. One of the many ways these oils increase inflammation and why they should be avoided at all costs on a well-formulated ketogenic diet for mental health. 

Ketogenic diets are great for inflammation, and I am sure those ketones are doing their work to help reduce it in your body. But you may have a pretty good buildup of it to deal with coming from the time before you changed your diet. You might need a little bit of help using supplements to calm things down and allow your body to heal. 

Some botanicals and supplements can reduce inflammation and help that inflammation cycle calm down to get the proper signals to stop making so much bile. These do not need to be taken long-term and probably should not be, and these would be short-term fixes to help your body get a handle on the inflammation contributing to the dysregulation of the bile-making process. And for goodness sakes, don’t take all of these at once. Take only one and see how it works for you.  

These are all affiliate links. Please do not feel obligated to use them. 

Ascorbic acid

Take 2-4g in divided doses to reduce oxidative stress in the intestines. You may only need to take this for a few days or a couple of weeks. 

Swanson Premium Vitamin C with Rose Hips

Milk thistle

(Silymarin + Silybilin) activates the FXR receptor and promotes FGF19, so it can tell the liver to stop making so much bile.


This does a ton of things and is a powerful supplement. It promotes FXR activation by modifying gut bacteria and has a long history of treating diarrhea. 

Swanson Premium Berberine


This botanical is made from the plant Artemisia and significantly increases the FXR receptor. It is also anti-microbial. If you have liver disease you should maybe skip this one.

Before you take any of these, please check with your doctor or seek a functional medicine professional to assist you. These powerful substances influence liver enzymes and may interact with your medications and other supplements.

As always, this blog is never medical advice.

If you are already on medications or taking other supplements, please check for potential interactions using one or both of these resources. 

Another supplement that may help reduce gut inflammation and help regulate this mechanism is one I wrote about in a previous article about OPCs. These substances are fantastic for neuroinflammation and also have strong effects in reducing gut inflammation. So this may be a great two-punch supplement for a ketogenic diet working towards better mental health.

I would take 1 of these 2x per day to reduce inflammation in the gut and help regulate bile production. 

Pure Encapsulations CurcumaSorb | Curcumin Supplement to Support Digestive, Liver, Brain, Muscles, Bones, and Cardiovascular Health* | 180 Capsules

For some people, Curcumasorb Mind may be prohibitively expensive. If that is the case, I would recommend a less expensive but still third-party-tested option. Swanson Grape Seed, Green Tea & Pine Bark Complex provides 125 mg each of grape seed, pine bark, and green tea.

Vitamin A or D deficiency

You may be Vitamin A and D insufficient or deficient. Even on a well-formulated ketogenic diet. Remember, you came into this dietary change sick and depleted. These vitamins play roles in suppressing bile-acid synthesis, and they repress liver expression of CYP781, which slows down bile acid synthesis. Slowing this down with sufficient levels of Vitamin A and D can be therapeutic for this condition. 

Vitamin A deficiency can be difficult to ascertain. If you have night blindness, some bumps on the back of your arms, or a weird coating on your scalp, you may be suffering from Vitamin A deficiency. You may need some functional testing to try to figure it out. But you can also carefully supplement to see if you can get those symptoms to go away. Chris Masterjohn, Ph.D., has a very helpful video about Vitamin A supplementation that I highly recommend. 

If you have not yet done a Vitamin D test, you really need to. Knowing your levels is so instrumental in your healing. Go to your doctor and get one. Or you can get a Vitamin D test by going to a lab near you using UltaWellness (affiliate link). 

Or, if you are too busy to get to a lab, you can have your functional practitioner order you a finger prick (Dried Blood Spot) test from Great Plains Laboratory (not an affiliate link).

Circadian dysregulation

Each organ system and cell have their own little clocks, and external stimuli help them decide when. Bile acid regulation is an ancient function in our biology, and it is highly tuned to circadian rhythms. 

You may need to eat at a different time because circadian regulation is related to bile acid production. You may be eating too close to bedtime (finish eating at least 2 hours before bed, longer is better).  

If your D levels are low, this disrupts circadian rhythm. 

Are you exercising after dark or too close to bedtime? That will also disrupt your circadian rhythms. 

Behavior changes that respect the light and dark cycles that your biology is made to be attuned with may do a lot to help your cells time their production and expression of bile acids. 

Paying attention to circadian rhythms is part of you healing your brain and why you are doing the ketogenic diet in the first place. So this may be a natural next step progression in your quest to know all the ways you can feel better. 

Another not well-known cause of mysterious digestive symptoms, including diarrhea is heavy metal toxicity. You may want to investigate it if you continue to have mysterious digestive symptoms, regardless of your diet.


Changing your lifestyle to heal your mental illness or neurological disorder is a big change. And sometimes obstacles can come up and you can use a little help getting past them. I wouldn’t want you to stop your ketogenic diet prematurely before the full benefits can be experienced because of things that can come up and you don’t have the support you need to solve them. Diarrhea is definitely one of them.

Loose stools are not your problem? But you have stomach bloating after you eat? Then you will want to read this post:

I want to support you on your wellness journey and help you learn all of the ways you can feel better. You may be experiencing other challenges in trying to adopt a ketogenic diet and you might benefit from these other blog posts.

I am a mental health counselor that works with dietary and nutritional therapies to treat mental illness and neurological issues. I use nutritional and functional psychiatry and testing in my practice. You can learn more about me here. Feel free to contact me on your journey to mental health.

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