The Ultimate Digestive Troubleshooting Guide: What to Do When Diet Isn’t Helping Your Stomach Problems


“How many of you started eating a real food diet, whether it’s Paleo, Weston A. Price, SCD, or GAPS, because of digestive problems?”

About 75% of the people in the room raised their hand. I was speaking at a Weston A. Price Foundation meeting and it shocked me to see so many hands in the air.

“WOW, ok. Please keep your hand up if you STILL have digestive problems, even though you’re eating a real food diet.”

Only a few hands went down… again, shocked!

So, if you’re eating Paleo, SCD, GAPS, or WAPF and still have stomach problems… you’re not alone. We get emails every single day from people struggling just like those at my talk. Maybe it’s annoying gas and bloating after meals, or bouts of agonizing constipation. Worse yet, maybe it’s gut-wrenching diarrhea that won’t stop. Any way you cut it, it’s frustrating to eat all the “right” foods and still deal with stomach problems.

What gives? How can you eat a nutrient dense, non-toxic, real-food diet and still feel bad?

Why Can’t One of These Diets Just Fix Everything?

We started SCD Lifestyle almost six years ago, we’ve helped 110,000+ people since then, and what I consistently found is that people would pick a diet (let’s say Paleo or SCD or Weston A. Price or GAPS), they would change their diet, commit to this change, and it wouldn’t work.

So they had put all their hope into changing their diet, they did everything they could to change their diet and then… it didn’t work. Their hope would be stolen from them because they tried it and it didn’t work.

What we found over the years is that really it’s about finding a custom diet that works for you. It’s about putting on your engineering hat, whatever that looks like for you.

We can all be health engineers.

So, we put on our engineering hats and we customize our diet. After all, we’re talking about troubleshooting digestion and how to get to the root cause of your health issues by avoiding some common mistakes and by calling upon some expertise. First, let’s look at common mistakes that occur on real food diets.

Mistake #1: Thinking SCD, GAPS, Paleo, or WAPF Will Work For You

The diet that will work for you has no name.

You have a custom solution.

You’re not going to be able to follow Breaking the Vicious Cycle and do SCD exactly as it’s laid out.

You’re not going to be able to pick up a Paleo book and follow that blueprint and have it work for you.

It’s just unrealistic. To get to the diet that works for you, you have to troubleshoot. You have to tweak. You have to be a health engineer!

It’s a different mindset…

I’m going to say this again: It is a different mindset.

It is so important to know that. There is no pre-written script that says follow these exact steps and your specific digestive problems will go away… and that makes it tough – it isn’t coming to you pre-packaged.

For example, some people don’t tolerate dairy. Others don’t tolerate legumes. Many don’t even tolerate fermented foods or food with high FODMAPs.

And that’s where people fail, that’s where the diet stops working and that’s where people lose hope. But if you keep your hope; if you change your mindset and keep your hope that YOU are a health engineer and YOU will figure this out, then you will succeed.

And so as you’re doing this, if you are embarking on the adventure that is your health,  to avoid mistake number one just know that you’re going to have to create a custom diet that works for you and it’s going to take some time. And that’s OK. So, chew on that, let it digest, and absorb this new idea before you embark.

You are like a snowflake.

As a kid, one of the most powerful insights I ever had was this idea that every snowflake is different.

We’ve all heard this analogy over the years. We’ve all heard the story about how there isn’t a single snowflake that’s like another in the entire world! This blew my mind as a child (second to only when I found out where babies come from).

It’s a powerful thing…

So, as you try different diets you just have to understand you are a snowflake, you are unique. Any diet recommendations I put on the website, or anyone else’s that you read, you just have to know that you’re going to have to make it a little bit different for you.

And it’s OK to play with it.

We don’t all get it right on the first try so keep exploring. Remember, you are a health engineer! Alright? Alright!

So, that’s the first thing I wanted to address: mindset.

Re-frame how you think about your diet – you are the engineer, you are the script writer – and your needs are going to be as unique as a snowflake.

Mistake #2: Not Listening to Your Body

Our bodies are always talking to us, but often we don’t really listen.

Have you ever been sick with a wicked flu?

Maybe you’re like me and your darling children brought it home from school just for you?

Imagine you have a fever of 103°F, you are hallucinating, just laying in bed and your body is like:

“Hey, I am actually doing you a favor – I’ve got your back, I know the fever sucks but I had to turn up the furnace a little bit – I’ve got to kill off this virus.”

Your body is taking care of you.

Now, I’ve been in this position and I remember thinking about when I was a kid and my mom would be like, “Your fever is too high! Tylenol, Tylenol, Tylenol!! We’ve got to get that fever down!”

And I just thought about my body when I was a kid talking to me like, “Hey, we’re trying to burn this thing out! Stop turning the fever off! You’re not letting me do my job!”

So, imagine you’re deep in this fever, your body is talking to you, and maybe in your hallucinatory state your mother’s words of “Tylenol, Tylenol, Tylenol…” are overlapping it and you reach out to grab some pills and you stop. You take a second to realize that a fever reducer is not what it needs.

Nowadays, we’re starting to know more. In this community, everybody can pretty much agree that we should not be reducing our fevers unless they become life threatening.

It’s a natural good thing your body is doing for you….

But what if ALL of our current symptoms are actually that way?

What if our diarrhea, fatigue, gas, or bloating are all clues from our body?

What if explosive diarrhea 10 plus times a day is your body’s way of sending out a flare signal like, “Hey, hey, I REALLY need some help here!!!”

But these days a bodily sign like gas, bloating, constipation, or diarrhea is a symptom that needs to be treated with a drug. Don’t worry that every time you eat bell peppers you get raging heartburn, just take a TUMS!

We’ve stopped listening. As a culture, we tend to ignore and gloss over with prescriptions and over the counter “cures” rather than actually trying to figure out what constipation, bloating, gas, headaches and other symptoms really mean in body speak. And that’s mistake number two:

Many of us ignore everyday symptoms in our body.

Just like when we have a fever, we ignore what our bodies are really saying. It’s just like when you have the stomach flu and are having crazy diarrhea; you need to get that infection out. Or when you drink too much alcohol and you throw up. Those are all natural things. Your body has your back.

Again, this is asking for a different mindset, one that is so different from what our current culture embraces. But our current culture is producing sick people. It is time for different thinking; it is time for change.

And we are changing things.

We’ve already talked about how you need to change your mindset to avoid mistake number one: not customizing your diet. Change things around until you find the glass slipper diet that fits you. There is no name for it. It’s real food tweaked to your body’s needs.

And we are also changing our mindset to begin to really listen to our bodies; to see symptoms as a sign of communication… not something to be stamped out or simply subdued. You have got to start listening to your body.

If you have gas, bloating, diarrhea, or constipation, your body is telling you something.

It’s like the check engine light in your car. How many of us have been in the car and we’re picking up the kids, we’ve got to go to soccer practice and it’s like ding, ding, ding and you’re like “Arrrrggghhh. Check engine light.”

And then it’s a week later, then it’s two weeks later and three weeks later and you start getting in the car in the morning and you’re hoping it still works like, “Come on baby you got this… vroom, yeah!”

It could be something simple, like maybe your gas cap is loose. That’s a common reason for the check engine light. But it could also mean your engine is going to blow up in the next five miles and you’re going to have a serious problem. You don’t know.

But it’s an indication that something is wrong. The check engine light is your car saying “Hey there’s a problem here; you need to get this worked on.” It’s got your back, just like your body. Look at your symptoms as clues, as hints of what you need to do to tweak.

Listen to your body and create that custom diet from the bodily feedback you receive. Maybe you are currently on the Paleo diet and you get really rocked when you eat sweet potato. This might not be a food that’s OK for you right now.

Try these real food diets to find out what does work for you. View your diet as a sounding board for your body. Use it as a starting point and proceed based on what your body tells you. Be sure to listen to your body.

OK, so we’ve got on our engineer hats and we’ve got our new mindset. But we’re still experiencing digestive trouble. It’s time to troubleshoot our digestion.

How to Troubleshoot Your Digestion (When Your Diet Isn’t Working)

Troubleshooting, hacking, engineering, designing… all of these words have really cool connotations to them and they all mean you’re in control. You’re in control of this thing; you’re in the driver’s seat baby.

If you have gas or diarrhea every day, you can take control and you can start to make things work for you to help those symptoms back off a little bit through healing rather than masking.

So, as we start to listen to these clues that our body is telling us, we can use them to understand whether or not what we’re doing is working on a day to day basis. That’s the beauty of the body; it changes and informs us every day. You can use this information to start troubleshooting your digestion and there’s three areas I want you to focus your attention on:

  1. Troubleshooting your food
  2. Troubleshooting your supplements
  3. Troubleshooting the root causes

Troubleshooting With Food

Why start with food? The bottom line: it’s something you can do tomorrow.

And that’s one of my goals: giving you a simple actionable step that you can use in your life tomorrow. So, if you’re having gas, bloating, constipation, diarrhea, nausea, if you’re having that in your life right now, you can go and make a change in your life tomorrow that is going to improve your symptoms. Action… taking action – that is what will bring about these changes we’ve been talking about.

In the real food community there are four foods that you should start your troubleshooting with first. We’ve nicknamed them The Four Horsemen, and if you know our work you know we’ve talked about them a bazillion times.

But that’s because these four foods are ones that people who jump right into a Paleo, or SCD, or GAPS, or WAPF diet experience trouble with the most. Oftentimes, it’s one of the Four Horsemen, NOT necessarily the rest of the diet, that doesn’t work for them. These first four foods can be cut out and can really reduce your symptoms quickly. I present to you… (drum roll please!!) THE FOUR HORSEMEN:

1. Dairy: Say what you will about dairy – there’s probably a lot of debate about it (especially in the Paleo-spheres) – but if you’re eating hard cheeses, if you’re eating Kefir, if you’re drinking raw milk, if you’re making 24-hour fermented yogurt, if you’re eating butter – if you’re eating these types of dairy products and still having digestive problems, then we’re talking Four Horsemen number one. Pull it out for three days and see how you feel. If you feel okay, you can bring it back in and see if you notice a difference.

2. Eggs: So, this is kind of an interesting thing because the albumenprotein in eggs (just like the casein protein in dairy) can be really problematic for people and cause a lot of immune response. It’s not really something we intuitively think about with eggs.

But if you’re like me you ate cereal every day for 20 plus years of your life and all of a sudden you switch to this real food diet and you’re like, “What do I eat for breakfast dude? What do you mean no Lucky Charms?” One of the first default places we go after kickin’ the breakfast cereal and toast is either bacon or eggs… maybe you do both.

If you start to find that you have this mysterious problem and your gut really acts up every day at about 10:00 AM, look at your breakfast first. Are you eating eggs every day? Because a lot of us do say, “No more cereal, I’m going to eat eggs every day.” So, eggs are the first place to look if you’re having weird symptoms every day around mid-morning, maybe right before lunch, like indigestion, gas, and bloating (that type of thing)…maybe some loose stool (for me I would get this horrible stomachache and a headache) it may be the eggs. But everybody is different, so pull them out for 3 days and see how you feel.

3. Nuts and nut flowers: So there’s two really common mistakes that happen with nuts and nut flours.

When I was working with people 1-on-1, I’d ask them specifically what they ate on Monday. Some people would walk me through their day and after we looked at it, it turns out they had 12 and a half handfuls of nuts.

Good Lord! That amount of nuts would probably make a healthy person have digestive problems. Have you ever dropped a nut on the ground? A lot of times a pistachio won’t even break when you drop it. Now, imagine trying to chew that same nut up and properly break it down if your digestion isn’t even working right.

Maybe you have a problem in your gut, or you have some damage going on, or you have leaky gut – any of those things – and you’re eating 12 and a half handfuls of nuts a day? Try stopping for three days and see how you feel.

Now on to nut flours. A lot of people (and I did this too) stop eating the standard American diet and start eating a real food diet but try to eat the same things like, “I’m going to make bread and I’m going to make pancakes and spaghetti and all these things I’m used to eating every day for the last 20 million years of my life! But I’m going to do it ALL with ALMOND flour.”

It’s really similar to the whole nut thing. I have somebody go through their diet on a Monday and all of a sudden I look and I’m like, “Wow! You ate nut flowers at every meal on Monday.”

That’s a lot of nut flour!

Again, you’re having subtle clues from your body that you’re having problems; you’re having this gas, diarrhea, constipation and stuff creeping up, then you want to make sure that you go in and pull those things out for three days. Give this a try and see how you feel.

4. Too much fruit and honey: Yup, I was guilty of this.

I couldn’t tolerate much when I first started out. All I could eat was puréed fruits and vegetables for a year. My gut was pretty banged up and I ate a lot of fruit. I’d eat avocado, but I’d pour honey all over it.

If, at the end of the day, you’re looking at your diet and realize, “Wow, I ate 5 bananas yesterday, good lord” – that’s too much.

Too much fructose and sugar can cause overgrowth of gut bacteria because you may have fructose malabsorption. Fructose malabsorption really just means not being able to absorb fructose. Fructose is a form of sugar and readily available in almost everything we eat, including fruit and vegetables. While fructose and glucose are different forms of sugar, they’re in the most simple form… but that’s the tricky part.  Both forms of sugar require no digesting at all, they are already broken down into the most simple form for the body to soak right up. Therein lies the problem behind fructose malabsorption; the fructose is not being soaked right up into the body.

So again, if you are having symptoms you may want to cut back on fruit and/or honey for three days.

Troubleshooting your food can be a really good place to start making changes tomorrow. If you’re having subtle (or not so subtle) clues from your body that it’s not working for you, start there. A lot of times you can even pull the Four Horsemen out all at the same time for three days. Then, you can bring them back in slowly, one at a time. And just so you’ll know for sure, go back to eating 3 bananas and see how you feel. Or you can bring that butter back, or maybe try having a handful or so of nuts – whatever it might be for you – and see how you feel over the next three or four days.

Troubleshooting with Supplements

A word of caution about supplements… to supplement literally means, “something added to complete a thing, supply a deficiency, or reinforce or extend a whole.”

Supplements are a “supplement” for a reason. They support the whole of a treatment plan. They plug holes and deficiencies to reinforce what we’re already doing.

So, if you’re reading this and haven’t customized your diet at all, the truth is supplements aren’t going to help much until you take your treatment plan seriously and start creating the custom diet that’s going to work for you.

If you’ve been troubleshooting your diet and you’re ready to take your health to the next level, I’m going to share some supplements that can really help you digest food better.

When we make the jump from the standard American diet to a real food diet, fat and protein intake go way up and carb intake generally goes way down. Along with these changes, we see a lot of people showing symptoms of low stomach acid, or hypochlorhydria.

A lot of times many people actually feel worse on a real food diet (which is a total bummer) because generally peoeple have too little stomach acid. This really effects your digestion and if you’re trying to digest real food, lots of fats and meats, and you don’t have enough stomach acid, your digestion becomes compromised. Stomach acid is a big first step in the digestive process.

So why is that?

Stomach acid is the great communicator. It starts digestion and sends the digestive message throughout your GI tract. Stomach acid regulates the pH level of your digestion and really dictates how well you digest food. When you eat food, your pH level goes up. In response, you secrete gastric acid and it starts to digest the food and bring the pH of your stomach back to a normal range of around 1 or 2.

If you don’t have enough stomach acid, you can’t regulate the pH of your stomach. And that’s a big issue, because that drop in pH is actually what tells your stomach to pass the food along to the small intestine. Once in the small intestine, the pH is what tells digestive processes to begin, like enzyme release. The pH communication line doesn’t stop there, though. It reaches all the way down to the large intestine.

So, if the stomach did its job right then the small intestine gets the right message, the large intestine gets the right message and so on and so forth.

Remember that game telephone – dates back to like kindergarten?

It would start out with someone saying something like,“Jenny likes the color blue.”  Then, they’d get down to the end and the last person would say out loud, “Jenny has the stomach flu!”


The communication is just totally screwed up between the nine kids that went around the circle. That’s what happens when your stomach acid is low; your body doesn’t get the right message.

So what are some signs you have low stomach acid?

If you’re someone who has undigested food in your stool, you have a lot of gas, bloating, diarrhea, constipation, acid reflux (a thread I keep repeating here today), you may have low stomach acid and are unable to properly digest the high amounts of meats and fats on this new real food diet. But guess what, for this there is a magic pill – I kid you not. Meet Betaine Hydrochloride – Betaine HCL. It’s stomach acid in a pill.

When I started taking Betaine HCL, I got perfect poops overnight. Seriously, the very next morning! It was like a magic pill for me. And I can’t tell you enough, but literally thousands of people with low stomach acid, who are eating more meat and just can’t seem to digest it, have read our work and taking that pill changes their lives.

But you need to be working with a skilled practitioner who understands Betaine HCL supplementation. If you have a history of ulcers or gastritis, a history of being on corticosteroids (I have to throw that disclaimer out there), then Betaine HCL might not be right for you.

Supplementing with stomach acid is not your ordinary run-of-the mill grocery store supplement; it’s serious business. I made a lot of painful mistakes taking Betaine HCL over the years. These mistakes can cause it not to work and make symptoms much worse than they already are, so work with a practitioner who knows what they’re doing.  It’s a very cheap supplement. It’s not sexy, but my gosh it helps people and it really helps with problems breaking down meat, or if you don’t feel good when you digest meat, it can really be a big thing for you.

Next, make sure you’ve got the ability to break down food.

The second supplement to explore while troubleshooting digestion is digestive enzymes.

Enzymes really happen as part of that cascade, as part of that telephone game of pH and stomach acid. So, start with the Betaine HCL and see how your symptoms react; see what your body says.

BUT if you’re like me and you have complete villus atrophy of the lining of the gut, meaning the villi are totally destroyed, then your brush border enzymes are going to be screwed up.

If your gallbladder has been removed, then your enzyme production might need support too. As previously mentioned, you’re increasing fat intake on a real food diet which means you’ll need an enzyme called lipase. Not only are we increasing our meat, but we’re increasing our fat. And if we don’t ramp up slowly or have a good adjustment of lipase production, we’re not going to digest fat very well. With that said, digestive enzymes can be really helpful too, especially for those with diarrhea. Digestive enzymes can transform stools overnight as well. Again, if you have ulcers or gastritis you really need to be careful about how you use and introduce them.

So, those are the two supplements in terms of troubleshooting your supplementation. And at this point, you’ve got some action steps for troubleshooting your food and supplements, but now it’s time to move on to one of the most critical… the root causes.

Troubleshooting the Root Causes

Your symptoms may go deeper than diet and supplements.

Most of us come to real food diets because we’re sick. Whether it’s autoimmune disease, heart disease, chronic fatigue syndrome… the list goes on. And during this article I mentioned the fact that many of us get on these real food diets, but we don’t get better.

The truth is, while changing your diet is the foundation of good health – and it’s incredibly important – it’s only the first step and it’s not always enough. Even if you dial in your diet – customize it for you – there may be more going on.

There may be a deeper cause and you need to get to the root of it.

You may have alleviated symptoms through diet and helped support your body with supplementation, but finding out the root cause of these problems is important for your long-term health. If just switching to a real food diet isn’t enough, there’s more work you have to do here – even beyond fixing the first two mistakes we talked about today. There’s more tweaking, engineering, and designing to do. There’s further to dig and you may need some help with that process.

And asking the following question could be the most important step in troubleshooting your digestion: what are some common root causes?

Here are some of the most prominent root causes that we see in the people we work with:

Number 1. Gut Infections

G.I. infections, gut infections, parasites, bacterial infections, small intestinal bacterial overgrowth, and gut dysbiosis can all be the root cause of issues you’ve been experiencing. Eighty percent of the people that we worked with one-on-one had positive parasitic or bacterial infections like:

These infections are found through stool testing, and just like practitioners not all stool tests are created equal. It’s really important to look for gut infections, especially if diet is not enough, if diet is not helping you to get better, or if it’s only half helping or three-quarters helping you.

What to do about it: Work with a skilled practitioner on this; one who understands how gut infections can be a root cause of health issues. We recommend ordering a BioHealth #401H GI Pathogen Screen With Pylori (stool test). If you can’t get a practitioner to order one of these for you, order one here.

Five years ago, I followed a STRICT diet of 7 foods and still struggled with diarrhea, then I got my stool test result and it came back with the words: “Strongyloides stercoralis.” It’s a parasitic roundworm infection and I had it.

Once I treated the infection everything about my health changed.

It’s almost like I’d been driving with one foot on the gas and one foot on the break the whole time, and now my health was going 100 mph toward a beautiful horizon. The parasite was there the whole time, wreaking havoc on my gut and preventing me from fully healing. It was a big step in my healing journey… not the only one of course, but a huge leap forward and it could be a root cause problem for you as well.

Number 2. Hormone dysregulation

Anytime we’re having hormone problems, the gut can have problems. Whether it’s adrenal fatigue, or thyroid problems, hormone dysregulation is a common root cause problem. Steve and I have both struggled with it and see it more and more in people we’ve worked with.

If your digestive symptoms are coupled with fatigue, headaches and weight gain you may be experiencing hormone dysregulation. Or, if you are under a lot of stress – the death of a loved one, a divorce, a crazy demanding work schedule or positive stress from a pregnancy or marraige – you may develop hormonal imbalances.

And we don’t just mean emotional stress. Maybe you’re a crazy crossfit gal and are tearing it up with high intensity intervals at the gym every day, or you’re an Ironman athlete and spend more time in the saddle than you do sleeping every week.

Physical stress, emotional stress, and any of these chronic stressors can alter your hormone balance and in turn really affect your gut. Hormones regulate your bodily systems; you may have heard them referred to as chemical messengers of the body and they are. Thyroid hormone in particular really plays a role in metabolism and how your body utilizes its energy. But there is an entire chain of command in hormone responses and any link could be off.

What to do about it: This is definitely where working with a skilled practitioner comes in. Just like stool testing, hormone testing is tricky; interpreting hormone tests is tricky. What may be “in-range” may not be optimal for you. Again, it all comes back to that snowflake and your biochemical individuality. I highly recommend ordering a Functional Adrenal Stress Profile like the BioHealth #201 Functional Adrenal Stress Profile. If you can’t get your practitioner to order one for you, you can order one here.

How to Start Troubleshooting Your Digestion Today

I’ve given you many action steps in this article and the most important thing you can do is to pick one and take action on it in your life right now.

Let’s recap the important troubleshooting steps:

  1. Mindset. Adopt a new mindset. Put your engineer hat back on. Remember, YOU are the engineer, the designer, the troubleshooter of YOUR health.
  2. Listen to your body. Listen to what it’s trying to do, it’s got your back and just know that. Use your symptoms as clues to help you troubleshoot.
  3. Troubleshoot your diet – build the diet that is right for YOU. Use your new mindset and “ears” that are tuned into your body to do this. Test out removing the four horsemen.
  4. Troubleshoot your supplements with Betaine HCL or Digestive Enzymes.
  5. Find a skilled practitioner who can help you with getting to the common root causes like gut infections or adrenal fatigue.

Most Important: Work with a Skilled Practitioner to Help You

Troubleshooting is challenging. It’s the secret to overcoming chronic illness, but it takes time to make mistakes and find what’s going to work for you.

Some of the most powerful health breakthroughs I experienced were because I was working with a skilled practitioner who knew how to help me troubleshoot.

You want to make sure the practitioner you link up with understands that you are a snowflake – seriously. You also want to make sure they know the RIGHT tests to order.

You could throw money randomly at the wall and order a battery of tests costing $3,000 to $8,000 like some of our 1-on-1 private clients have told us about. Or you could check into some of the world-renowned clinics you’ve probably heard of for $10,000 to $20,000…

Alternatively, you can work with skilled practitioners, most of whom have battled back from their own sickness, to find out what the right tests are to peel back each layer.

A skilled practitioner can help find the right tests for you… and help you discover the root causes of your illness. We want to empower you in your health. Adopt your new mindset, tweak your diet and keep re-tweaking based on what you hear your body tell you. But also understand you can’t address a root cause if you don’t know it’s there.

If you’re still experiencing problems after troubleshooting your diet, don’t give up. Contact a skilled professional who can figure out those root causes and work with you to fix them. We are here to support you along the way because we have been there too. Working with a Functional Medicine practitioner may be what it takes to get you out of there, over that final hump, to fix that root cause and restore your optimal health.

Not sure where to find one? We’ve built relationships with skilled Functional Medicine practitioners for you… you can book an appointment with one of them right now here:


No matter what, don’t give up hope. Hope is all you have… it’s a choice to keep it and never give up the fight. You CAN get through this. Never give up your hope… it’s the secret tool you have to get through anything, including overcoming your chronic illness.

Know that I believe in you!

– Jordan

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