Best Foods to Restore a Leaky Gut & Microbiome

Your gut is at the center of your health. It’s where digestion, immunity, nutrient absorption, and even mood regulation begin. But when your gut lining becomes damaged—a condition known as leaky gut or intestinal permeability—it can allow toxins, food particles, and pathogens to enter the bloodstream and trigger inflammation throughout the body.

Leaky gut is often linked to symptoms like bloating, fatigue, food sensitivities, brain fog, and even autoimmune conditions. A damaged gut also disrupts your microbiome, the trillions of bacteria that help regulate digestion, immunity, and overall health.

The good news? Healing starts with food. The right foods can soothe inflammation, repair your gut lining, and nourish the good bacteria that keep your microbiome in balance.

Important note: While food is a powerful tool, healing leaky gut naturally through diet alone may not fully address deeper issues like dysbiosis, bacterial overgrowth, or nutrient deficiencies. These conditions often require targeted supplements, functional stool testing, and personalized care. Think of these foods as a supportive foundation—a strong first step to start moving your gut in the right direction.

Here are 7 of the best foods to restore a leaky gut and support a thriving, healthy microbiome:

1. Bone Broth

   
   

Bone broth is a powerful gut-healing staple. Made by simmering animal bones with herbs and vegetables for hours, bone broth is rich in collagen, gelatin, glycine, and glutamine—all essential nutrients for repairing the gut lining.

• Collagen and gelatin help strengthen the gut wall and improve its integrity.

• Glycine and glutamine support cell regeneration and reduce inflammation in the intestinal lining.

  
  

Tip: Sip warm bone broth as a nourishing morning or afternoon drink, or use it as a base for soups, stews, or even cooking grains

2. Fermented Foods

   
   

Fermented foods are natural sources of probiotics, the beneficial bacteria that help crowd out harmful microbes, support digestion, and strengthen the immune system.

When your microbiome is in balance, your gut lining can heal more effectively. Fermented foods also produce short-chain fatty acids (SCFAs), which reduce inflammation and support gut barrier function.

Top fermented foods to include:

• Kimchi

• Sauerkraut (unpasteurized)

• Kefir (dairy or coconut-based)

• Yogurt with live cultures

• Miso and tempeh

• Kombucha (with minimal added sugar)

Note: If you have SIBO or gut overgrowth, some fermented foods may worsen your symptoms—it's important to listen to your body and seek testing if you feel worse after introducing probiotics.

3. Fermented Foods

Prebiotics are the food for your probiotics. These are types of fiber and resistant starch that aren’t digested by you—but are fermented by the good bacteria in your colon, helping them grow and thrive.

A diet rich in prebiotics can support microbial diversity, reduce inflammation, and improve gut barrier function.

Excellent prebiotic foods:

• Garlic

• Onions

• Leeks

• Asparagus

• Artichokes

• Green bananas and plantains

Tip: Add sautéed onions and garlic to your meals daily, or roast artichokes and asparagus as a gut-friendly side dish OR consider adding an unripe banana into your daily protein shake or smoothie.

4. Omega-3 Fatty Acids

Chronic inflammation is a key driver of leaky gut—and omega-3 fatty acids are powerful anti-inflammatory agents that help calm the immune system and support gut repair.

They also play a role in maintaining the integrity of cell membranes, including those that line the gut.

Top omega-3 sources:

• Fatty fish like wild-caught salmon, sardines, mackerel

• Chia seeds

• Flaxseeds (ground)

• Walnuts

• Algae-based omega-3 supplements (for plant-based diets)

Tip: Aim to eat wild-caught fatty fish 1–3 times per week or add ground flaxseed in smoothies, oatmeal, or salads.

5. Collagen and Gelatin

Collagen is one of the most abundant proteins in the body, and it’s especially rich in amino acids that support the gut lining, including proline, glycine, and glutamine. These nutrients help rebuild the intestinal wall and promote tissue repair.

Gelatin, which is derived from collagen, has similar gut-healing benefits and can be a gentle way to soothe an irritated digestive tract.

Gut-healing collagen sources:

• Chicken skin

• Pork skin

• Bone broth

• Collagen peptides (powder)

• Gelatin-based desserts (look for clean, low-sugar versions)

Tip: Try adding a scoop of grass-fed collagen powder to your morning smoothie or tea.

6. High-Fiber Vegetables and Fruits

Fiber is essential for digestion and gut health. It promotes regular bowel movements, feeds good bacteria (especially when it's prebiotic), and supports detoxification.

A diverse fiber intake also encourages microbial diversity, which is linked to better gut resilience and immune function.

High-fiber gut-friendly options:

• Leafy greens (spinach, kale, arugula)

• Carrots, beets, zucchini

• Berries (blueberries, raspberries, blackberries)

• Apples with skin

• Sweet potatoes

• Lentils and chickpeas (if tolerated)

Tip: Eat the rainbow! The more variety of plant foods you include each week, the more diverse your microbiome will be.

7. Turmeric and Ginger

These two roots are celebrated for their powerful anti-inflammatory and antioxidant properties, both of which are essential for calming the gut and reducing symptoms of leaky gut.

• Turmeric contains curcumin, which has been shown to help reduce gut inflammation and support microbiome balance.

• Ginger soothes the digestive tract, stimulates bile flow, and can reduce bloating and nausea.

Easy ways to use turmeric & ginger:

• Add fresh grated ginger to hot water with lemon

• Sprinkle turmeric into soups, curries, or roasted vegetables

• Blend both into smoothies or golden milk lattes

Now that your gut is calmer and less inflamed, you can begin to rebuild and repair the gut lining with specific nutrients known for their gut-healing properties.

 Key nutrients to support gut repair:

• L-glutamine: An amino acid that helps rebuild the intestinal lining

• Zinc: Supports immune function and tight junction integrity

• Omega-3 fatty acids: Help reduce inflammation and promote healing

• Collagen: Provides the building blocks for gut tissue repair

Healing foods to incorporate:

• Bone broth (rich in collagen, gelatin, and amino acids)

• Fermented foods (see below for more on probiotics)

• Wild-caught fatty fish

• Pumpkin seeds, oysters, and lentils (great zinc sources)

• Grass-fed gelatin or collagen powders (add to smoothies or tea)

These nutrients help restore the gut lining’s strength and flexibility, which is key to reducing permeability and improving nutrient absorption.

Conclusion: Your Gut Can Heal—One Bite at a Time

Healing leaky gut and restoring a balanced microbiome isn’t about perfection—it’s about consistency and nourishing your body with the right tools.

To recap, here are the best foods to restore gut health:

1. Bone Broth

2. Fermented Foods

3. Prebiotic-Rich Vegetables

4. Omega-3 Fatty Acids

5. Collagen and Gelatin

6. High-Fiber Fruits and Vegetables

7. Turmeric and Ginger

Incorporate a variety of these healing foods into your diet each week to calm inflammation, support repair, and rebalance your gut microbiome.

At Solara Functional Wellness, we take a root-cause approach to healing gut issues naturally and sustainably. If you're experiencing persistent symptoms like bloating, fatigue, food sensitivities, or skin issues—it may be time for personalized support and advanced testing.

Healing a leaky gut isn’t about overnight changes or rigid protocols—it’s about consistently removing what harms your gut and adding in what helps it heal.

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References: 

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Costantini, L., Molinari, R., Farinon, B., & Merendino, N. (2017). Impact of omega-3 fatty acids on the gut microbiota. International Journal of Molecular Sciences, 18(12), 2645. https://doi.org/10.3390/ijms18122645

Leeuwendaal, N. K., Stanton, C., O'Toole, P. W., & Beresford, T. P. (2022). Fermented foods, health and the gut microbiome. Nutrients, 14(7), 1527. https://doi.org/10.3390/nu14071527

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Thakur, V., Bhatt, R., & Wani, A. A. (2024). Modulating gut microbiota through functional foods: Recent advances and future perspectives. Trends in Food Science & Technology, 143, 416–432. https://doi.org/10.1016/j.tifs.2024.02.012

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Zhou, X., Afzal, S., Wohlmuth, H., Münch, G., Leach, D., Low, M., & Li, C. G. (2022). Synergistic anti-inflammatory activity of ginger and turmeric extracts in inhibiting lipopolysaccharide and interferon-γ-induced proinflammatory mediators. Molecules, 27(12), 3877. https://doi.org/10.3390/molecules27123877