How to Heal Your Gut Naturally: A Clinician’s Guide

• Gut Health Basics|
• Reset the Gut|
• Gut-Healing Supplements|
• Remove Lingering Microbes|
• Rebalance Digestion|
• Reintroduce Foods|
• Nourish & Maintain|

How to Heal Your Gut: A Quick Snapshot

The first step to healing your gut naturally can start with reducing digestive overload and identifying food triggers. From there, probiotics and targeted interventions may help stabilize symptoms, and additional steps are only necessary if progress stalls. The framework below shows where to start and when to move forward.

A structured, clinician-backed framework for restoring gut health naturally:

1. Reset the gut environment through targeted elimination and symptom reduction
2. Support a resilient foundation with gut-healing supplements
3. Address lingering microbes with herbal antimicrobials (when needed)
4. Rebalance digestion using a natural prokinetic (if GI tract movement is slow)
5. Reintroduce foods strategically to expand tolerance
6. Nourish and maintain long-term gut health

Poor gut health rarely shows up as just digestive discomfort. For many people, and oftentimes in clinical practice, it can overlap with symptoms such as fatigue, brain fog, disrupted sleep, skin changes, and food reactions.

This guide outlines a clear, step-by-step framework for healing the gut naturally, based on clinical experience and the best available evidence.

Everyone’s gut-healing journey is different, but this framework can help clarify where to begin and how to progress.

Gut Health Basics 

The gut plays a central role in digestion, nutrient absorption, immune regulation, and inflammatory signaling throughout the body.

For this system to work well, alignment is crucial for each and every part. To begin, stomach acid and digestive enzymes need to break food down efficiently before it reaches the small intestine. After this, the intestinal lining must allow nutrients in while keeping potential threats out.

Beyond this, a healthy gut relies on a diverse community of microorganisms, known as the gut microbiome. These microbes support digestion, help regulate inflammation, and protect the gastrointestinal lining 1.

When gut function is disrupted, nutrient absorption may be impaired, inflammation can rise, and immune signaling can become dysregulated 2. As a result, gut issues often extend beyond the digestive tract.

Common Signs of Poor Gut Health

Research has identified associations between gut dysfunction and a wide range of digestive and non-digestive symptoms, including:

• Food intolerances 3
• Fatigue 4
• Mental health symptoms such as depression or anxiety 5
• Brain fog 6
• Insomnia 7
• Skin conditions such as acne 8, rosacea 9, eczema 10, or psoriasis 11
• Female hormone-related symptoms, including premenstrual syndrome (PMS), polycystic ovary syndrome (PCOS), abnormal cycle length or flow, low libido, or hot flashes 12
• Male hormone imbalances, showing up as fatigue, low libido, erectile dysfunction, muscle loss, and poor memory 13
• Weight loss 14
• Dry or thinning hair 15
• Joint pain 16
• Autoimmune thyroid disease 17
• Celiac disease or gluten intolerance 18
• Histamine intolerance 19

These associations do not mean the gut is the sole cause of every symptom, but they do highlight the gut as a logical starting point.

The encouraging part: the gut is highly adaptable. With the right foundations in place, gut function often improves and symptoms can become more manageable.

How to Heal Your Gut Naturally: A 6-Step Clinical Framework

This framework reflects the same gradual approach I outline in Healthy Gut, Healthy You, adapted here to clarify how each step fits together.

Keep in mind, not all steps are necessary for everyone. Many people experience meaningful improvement early on. The goal is not to do more. The goal is to find what your gut actually needs, in an order that supports progress.

Step 1: Reset (Pause Digestive Overload)

A gut reset is designed to temporarily reduce digestive workload and inflammatory input so symptoms can calm and the gut can begin to recover.

This step is foundational. For many people, meaningful improvement starts here. Think of it as taking pressure off an overworked system.

Reduce Digestive Workload

For some people, especially if symptoms feel intense or unpredictable, a short liquid reset can help stabilize digestive function more quickly.

This usually means taking a brief pause from solid food for one to four days and focusing on consuming bone broth or an elemental diet. Bone broth is accessible and works well for some. However, those who may be reacting to FODMAPs (which we’ll discuss shortly), might want to consider a low FODMAP-friendly variation. Personally, I enjoy Fond’s Chicken Bone Broth with Turmeric & Black Pepper. It’s low FODMAP and turmeric has additional gut health benefits. That being said, in my experience, elemental diets tend to be more reliable.

An elemental diet is a nutritionally complete shake made with pre-digested ingredients. Because the nutrients are already broken down, the digestive system requires less effort to process them. This reduced workload alone can make a noticeable difference when digestion feels overwhelmed.

Elemental diets were originally developed as medical nutrition, and they are well-studied. Research suggests they may help reduce inflammation and limit bacterial overgrowth, which is why they are often useful during a reset 20 21.

However, the liquid reset is an optional tool, not a requirement.

What is foundational in this first step is dialing in an anti-inflammatory elimination diet for a defined amount of time. The most meaningful change can be observed at this point.

An elimination diet works by temporarily removing foods that are most likely to irritate the gut, fuel overgrowth, or trigger symptoms. By lowering that background “noise”, digestion has a chance to settle, making symptoms easier to identify.

Two approaches tend to work especially well 22:

1. Paleo Diet: This diet removes foods that are commonly associated with gut irritation like refined grains, added sugars, and ultra-processed ingredients. Whole and nutrient-dense foods are emphasized, with choices guided by individual tolerance.

If this sounds like the right fit, you can find the step-by-step process in my Paleo Diet Guide.

2. Low-FODMAP Diet: This diet can alternatively be a better fit when bloating, gas, or food-triggered symptoms are prominent. This approach temporarily reduces fermentable carbohydrates that may aggravate a sensitive digestive system or a gut with bacterial overgrowth. 

For step-by-step guidance, see my Low FODMAP Diet Guide.

Stabilize Daily Inputs

While the diet does a lot of the heavy lifting, it does not work in isolation.

During a reset, the goal isn’t to optimize every habit—it is to establish stability. Supporting sleep, easing stress when possible, and keeping movement gentle and consistent can help reinforce dietary changes and reduce symptom volatility 23 24 25.

Small adjustments can make a meaningful difference, especially when the gut is already sensitive.

If symptoms improve substantially after several weeks at this stage, stopping here can be an appropriate and successful outcome. 

Step 2: Gut Healing Supplements (Start with Probiotics)

Probiotics are a good starting ground when searching for gut-healing supplements.

Along with diet, probiotics can be considered one of the most reliable tools we have for restoring gut balance. Both research and clinical experience support their role as a foundation for gut healing 26.

Probiotics

Probiotics are beneficial bacteria and yeast that help support gut balance, aid digestion, and modulate immune function. Beyond their supplement form, you may know of them from foods like yogurt, kimchi, and kombucha. They work by promoting a healthy microbial community, competing with harmful microbes, and producing compounds that influence gut and systemic health 27.

When They’re Helpful

Most people who are working to heal their gut can benefit from probiotic supplementation. If diet changes alone haven’t been enough to calm symptoms, probiotics can be considered as the next step.

How to Use

Probiotic benefits can be both strain-specific and symptom-specific, meaning no single strain works best for every digestive issue. Research shows that both single-strain and multi-strain probiotics can be effective, depending on the symptom being targeted (such as pain, stool consistency, or quality of life). Because many people experience multiple overlapping gut symptoms, a multi-strain, triple-therapy probiotic is designed to support a broader range of digestive functions rather than focusing on just one outcome.

For that reason, we focus on broader support rather than micromanaging the gut microbiome. Our Triple Therapy Approach was developed to cover the most important probiotic categories and offer the widest range of benefits. That being said, you don’t need to focus on getting everything “just right” during your gut health improvement journey. Consistency matters far more than precision.

One important thing to keep in mind is timing. Most research suggests it can take around two months to see the full benefit from probiotics. Not noticing major changes right away doesn’t mean they are not working. Give probiotics some time before deciding if it’s best to pursue other options.

Digestive Enzymes or Acid

Digestive enzymes help break down carbohydrates, proteins, and fats so food can be absorbed more efficiently. Stomach acid plays a similar role, especially early in the digestive process, by helping activate enzymes and prepare food for absorption.

Some peoples’ bodies don’t make enough of the enzymes required to break down carbohydrates, proteins, or fats. This can lead to bloating, gas, abdominal discomfort, or unpleasant bowel movements. 

When They’re Helpful

Digestive enzymes or stomach acid support may be helpful for those following a gut-focused diet and taking probiotics, but who still notice symptoms after eating.

This can present as bloating, gas, heaviness, abdominal discomfort, or feeling like food just “sits” in your stomach. These symptoms don’t necessarily mean something is seriously wrong, but can often reflect under-supported digestion.

How to Use

Taking digestive enzymes that include amylase, protease, and lipase at the start of a meal may reduce symptoms like burning, pressure, early fullness, bloating, or nausea, which are often grouped under functional dyspepsia, and may improve quality of life 28. 

In some cases, low stomach acid may also be contributing. When appropriate, betaine HCl can be used cautiously to support digestion and nutrient absorption 29. This is something to approach thoughtfully, particularly for people who are prone to upper GI tract irritation.

For more information, check out my video explaining how to try HCl safely and effectively.

Supplements to Heal the Gut Lining

Sometimes, even when you are eating carefully, using probiotics, and supporting digestion, symptoms persist. Foods may not be tolerated as expected, and small deviations can lead to larger reactions. This can be confusing or discouraging, especially after you have already put in significant effort.

When this happens, the issue may not be what you are eating anymore. Instead, it may point to how supported your gut lining is.

The gut lining acts like a filter. When it’s under strain, that filter gets less selective (leaky gut syndrome). Things that normally might not bother you can suddenly trigger symptoms, and your system can feel stuck in a reactive loop. Here are the top supports. 

L-Glutamine

The cells that line your intestines use glutamine, also known as L-glutamine (the most abundant naturally occurring amino acid in the human body), as a primary fuel source. When the gut is irritated or inflamed, those cells burn through glutamine faster than usual to meet the increased energy demands of repair and immune activity.

Supplementing it is essentially giving those cells extra fuel to repair and regenerate, which can help the lining feel less irritated over time 30.

Used When: This is a good fit when symptoms feel like active gut irritation, or when IBS-type symptoms are flaring, especially during periods of high stress or heavy training when your gut feels more sensitive than usual 27.

Colostrum

Colostrum is the first milk produced after birth. Supplemental colostrum is typically bovine (cow-derived). It contains immune and growth factors that help strengthen the gut barrier and support immune balance in the gut 31.

Colostrum supplementation can be helpful when reactions feel immune-driven, like foods suddenly irritating your gut for no clear reason. It can be used to help the gut barrier feel more supported and less reactive 31.

Used When: This is often a better fit when symptoms appear immune-reactive, such as food sensitivities that don’t follow a clear digestive pattern, inconsistent reactions to the same foods, or gut symptoms that seem tied to immune activation rather than digestion alone 32.

Zinc (or Zinc Carnosine)

Zinc is a mineral involved in tissue repair and immune regulation and plays a direct role in maintaining and repairing the intestinal barrier 33. Zinc carnosine, a compound made up of zinc and the amino acid L-carnosine, tends to stay in contact with the gut lining longer and is often used for GI support 34 35.

Used When: This is most often considered when healing feels slow, such as symptoms lingering longer than expected, flares taking a long time to settle, or the gut feeling fragile rather than acutely inflamed 36.

These supplements are not intended for long-term use. They are typically used for a defined period to help restore digestive stability and predictability.

For a deeper look at these options, including which may be the best for you and supporting research, take a look at my Leaky Gut Supplements Guide.

Supplements to Reduce Inflammation

At this point in the process, many people may experience meaningful improvement, but symptoms may not be fully resolved.

Digestion may be more predictable and reactions less intense, yet symptoms still linger or flare with minor triggers. While the gut lining may be healing, inflammatory signaling may remain elevated.

This is where anti-inflammatory support can be helpful. Not because a new problem has emerged, but because the system still needs help normalizing residual inflammatory signaling.

There is no need to distinguish between ‘gut lining issues’ and ‘inflammation’ to apply this step. In practice, this phase focuses on addressing remaining inflammatory drivers once the foundational support is in place.

How to Use

Anti-inflammatory supplements are used selectively and temporarily, with the goal of helping inflammatory activity settle rather than layering on more long-term support.

Options commonly considered include:

• Vitamin D, which plays a role in immune regulation and inflammatory balance 37 
• Quercetin, a plant-derived compound studied for its anti-inflammatory and immune-modulating effects 38
• Collagen, which may support tissue repair and help reduce inflammatory stress in the gut lining 39
• Curcumin, a concentrated compound from turmeric that has been widely studied for its effects on inflammatory signaling 40

These supplements are best introduced one at a time for about 2–3 weeks, ideally with the help of a practitioner. If a supplement is producing clear benefits for you, it may be worth continuing. If there is no noticeable benefit or makes you feel worse, it’s okay to stop.

Step 3: Remove Lingering Microbes 

This step should be considered by those who have not yet experienced symptom relief and a reduction in inflammatory stress after resetting the gut and continued probiotic use. For this step, we use herbal antimicrobials to eliminate harmful microbes that persist in the gut after the first two steps. 

Research has shown that herbal antimicrobials may be just as effective as rifaximin–the prescription antibiotic that many doctors often use to treat small intestinal bacterial overgrowth 41. Herbal antimicrobials are also used in cases where the treatment of fungi and parasites is necessary.

When our clients start taking herbal antimicrobials, it is recommended that they continue following the diet that yielded beneficial results in the gut reset step and continue on the course of probiotics (with or without other supplements) that improved symptoms during the second step. 

Our antimicrobial protocol is designed to run for two months. During the first month, two antimicrobial formulas are used. In the second month, these are replaced with two different formulas, as outlined below:

For our clients who tend to be more sensitive to supplements, each antimicrobial formula is introduced one at a time. This allows tolerance to be assessed before adding the next formula, typically after a few days.

When beginning herbal antimicrobials, some clients may experience a temporary symptom flare  lasting several days to about one week. This may present as fatigue, irritability, headaches, flu-like symptoms, digestive discomfort, or changes in bowel habits. 

These responses are generally short-lived. However, if symptoms persist beyond a week or continue to worsen, this may indicate poor supplement tolerance, and the protocol should be reassessed.

Step 4: Rebalance Digestion

Once harmful gut microbes have diminished, if digestion is still sluggish (often showing up as constipation), we have found that natural prokinetic supplements may be helpful. Options such as peppermint oil 42 or ginger 43 are commonly used to help improve motility. This helps food move through the digestive tract at a healthier pace and can reduce stagnation that leads to bacterial overgrowth.

When digestion is running smoothly again, the next step is to start gently expanding the diet.

Step 5: Reintroduce Foods

Once symptoms are significantly calmer, the focus shifts from strict elimination towards rebuilding confidence and flexibility with food.

Reintroduction provides a structured way to see what your gut can tolerate now, without going through heaps of guesswork. It helps ensure that early dietary restrictions, as seen in the first step, do not become long-term by default.

How to Reintroduce Foods (Without Overcomplicating It)

Begin by reintroducing one food at a time. Pick something you genuinely miss, something realistic to eat, and something worth testing. I often suggest starting with the food you’ve missed the most, so the process feels less restrictive.

A simple approach might look something like this: On day one, try a small amount of the food of your choice. The second day, increase to a moderate portion size. And on the third day, try to eat a normal portion and see how you feel.

If you tolerate it well, that food can usually stay in your regular rotation. Alternatively, if your body is not tolerating it, you may experience various reactions.

For help navigating this process, check out my Food Reintroduction Guide. 

What Counts as a Reaction?

Reactions may not always be abrupt or obvious. Try to pay attention to changes in 44:

• Bloating, gas, or abdominal discomfort
• Stool changes (looser, constipation, urgency)
• Reflux or nausea
• Skin flares (redness or rash, hives, acne breakouts) 45
• Brain fog, fatigue, or sleep disruption 4

If You React, Here’s What to Do

A reaction, unless allergy-related, does not mean you need to completely cut this food out of your life. It may mean your gut isn’t ready for it yet.

If symptoms flare, you can go back to your limited diet for a few days and let any reactions settle. From there, either try a different food or gradually retest the same one later.

This is how you build a diet that is both gut-friendly and enjoyable.

Reintroduction is not a pass or fail test. It’s a way to get your life back, one food at a time.

Step 6: Long-Term Nourishment & Maintenance

The final step in my clinical framework to achieve a healthy gut is to return to a sustainable baseline. This includes gradually reintroducing all foods, even the more challenging ones to assess tolerance. Remember it’s important to be intentional with reintroducing certain foods. For example, prebiotic-rich foods like legumes, onions, and whole grains contain fibers that beneficial gut microbes feed on, but too much too soon can overwhelm the gut and trigger symptoms 46. 

This stage is also an opportunity to reduce supplements to a minimum maintenance dose. 

In the clinic, I often recommend halving each supplement dose over time. If a client reaches a point where symptoms return or they don’t feel their best, they can return to the previous dose. Many find they only need one or a few supplements long-term to maintain optimal gut function.

Start With the Foundations to Heal Your Gut Naturally

Poor gut health can affect digestion, energy, and overall vitality. Learning how to heal your gut naturally can help you regain a better quality of life and improved health.

When embarking on any gut-healing journey, it’s best to focus first on diet and lifestyle changes for a few weeks, and then consider probiotics if symptoms persist. 

If these initial steps aren’t quite enough, taking additional steps may be helpful. Adding digestive supports, inflammation-fighting supplements, and herbal antimicrobials may be necessary for improvement.

Remember: Gut healing isn’t about perfection. Setbacks are normal, and progress may not always be linear. If you decide to follow this guide, please don’t forget to reintroduce foods! I encourage my clients to include as many different healthy foods as possible in their diet. At the end of the day, a colorful and diverse diet is key to nourishing long-term gut health.

We’d be happy to support you on your gut-healing journey, so please reach out to our clinic if you’d like guidance.

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