You’ve learned what leaky gut is and how stress disrupts the gut-brain axis. Now let’s talk about how to heal leaky gut naturally using functional medicine.
Your gut has an incredible ability to regenerate when you remove irritants and provide the right nutrients, lifestyle, and microbiome support.
Your gut has an incredible ability to regenerate. Functional medicine helps uncover the why behind intestinal permeability and uses nutrition, lifestyle, and advanced therapeutics to rebuild integrity from the inside out.
Why Gut Healing Is More Complex Today
Modern life challenges your digestive system daily. Constant exposure to environmental toxins, ultra-processed foods, chronic stress, and sleep disruption can all weaken the gut lining.
Even “healthy” lifestyles face soil depletion and repeated antibiotic use that diminish microbial diversity.
The good news: your body is designed to heal when you remove the insults and supply the right nourishment.
The Four Core Steps to Heal Leaky Gut
Think of your gut as a living garden within you, a complex ecosystem that needs balance, nourishment, and care.
When the soil (your microbiome) is rich and diverse, the plants (your intestinal cells) grow strong and resilient.
When it’s depleted or overrun with weeds, inflammation takes root and the entire system struggles.
Here’s how to weed, feed, plant, and tend that internal garden so your whole body can thrive.
Step 1: Weed Your Garden – Remove What Harms Your Gut
This is where you take an honest inventory and remove toxic influences that may be hurting your gut.
For 30 days, I guide my patients through an elimination phase that removes the most common irritants to the gut barrier:
- Added sugars and artificial sweeteners
- Refined grains and gluten
- Alcohol
- Conventional dairy
- Processed foods and industrial seed oils
Each of these can drive inflammation, feed pathogenic microbes, or disrupt the tight junctions that keep your intestinal barrier intact.
After this foundational reset, we slowly reintroduce foods to discover your personal triggers and build a long-term, nourishing way of eating.
Step 2: Amend Your Soil – Nourish Your Body
Your intestinal lining renews itself every few days, but only if you provide the right building blocks.
Top gut-healing foods
- Bone broth – collagen, glycine, and glutamine for epithelial repair
- Colorful vegetables (7–10 servings/day) – antioxidants and prebiotic fiber
- Polyphenol-rich foods – berries, green tea, olive oil, pomegranate
- Healthy fats – avocado, extra-virgin olive oil, wild salmon
Key nutrients
- L-glutamine – primary fuel for enterocytes
- Zinc carnosine – strengthens tight junctions
- Magnesium + B vitamins – support energy metabolism
- Butyrate / tributyrin – a short-chain fatty acid that fuels colon cells and tightens the gut barrier
Step 3: Plant New Seeds – Reinoculate the Microbiome
A thriving microbiome produces short-chain fatty acids (SCFAs) such as butyrate, acetate, and propionate that calm inflammation and reinforce barrier strength.
Ways to boost SCFAs
- Eat prebiotic fibers (onions, leeks, asparagus, garlic)
- Add resistant starches (cooled potatoes, rice, green plantains)
- Include fermented foods (sauerkraut, kimchi, kefir, kombucha)
- Use a multi-strain probiotic if tolerated
Probiotic-rich foods that Heal Leaky Gut:
- Cultured vegetables
- Plain, organic cultured yogurt and kefir (if you’re not sensitive to dairy)
- Kombucha
- Kim-chi
How to Choose a Quality Probiotic Supplement
- Look for at least 50 million CFUs
- Look for a multi-strain probiotic that’s pharmaceutical grade
- Make sure your supplement has both probiotics and prebiotics
Step 4: Repair and Tend – Strengthen and Maintain
After you’ve cleared irritants and replanted beneficial microbes, it’s time to seal, soothe, and strengthen the gut barrier. This is where mucosal repair truly begins.
Foundational foods and nutrients that nurture your mucosa:
- Bone broth (1–3 cups/day): provides collagen, glycine, and glutamine — key amino acids for rebuilding the intestinal lining.
- Aloe vera juice (¼–½ cup/day): gently soothes inflammation and supports regularity.
- DGL (deglycyrrhizinated licorice): calms irritation and supports mucin production, your gut’s natural protective layer.
- L-glutamine: the preferred fuel for enterocytes, the cells that form the intestinal lining.
Advanced support for mucosal integrity:
- Tributyrin (butyrate): a short-chain fatty acid that energizes colon cells, tightens tight junctions, and reduces inflammation.
- Zinc carnosine: a clinically studied compound that accelerates epithelial healing and protects against oxidative stress.
- N-acetyl glucosamine (NAG): supports mucin synthesis and has been shown to aid intestinal repair in inflammatory conditions.
- Polyphenol-rich foods (berries, green tea, pomegranate): strengthen the mucosal barrier through antioxidant and prebiotic effects.
These nutrients help you heal leaky gut naturally by restoring mucosal integrity and reducing inflammation.
Are Peptides a Natural Way to Heal the Gut?
You’ve probably heard about peptides like BPC-157, KPV, or GHK-Cu being used for gut repair and wondered whether they’re “natural.” The short answer is yes, biologically speaking.
Peptides are short chains of amino acids that your body already produces to communicate healing signals between cells. They tell tissues when to regenerate, regulate inflammation, and strengthen the immune system. Therapeutic peptides simply mimic these natural repair mechanisms, helping your body do what it’s already designed to do.
In functional medicine, peptides aren’t replacements for the foundations of healing: nutrition, microbiome balance, and stress regulation, but rather adjunct tools that can accelerate repair once those basics are in place. When prescribed appropriately and sourced from a licensed compounding pharmacy, they can be both safe and remarkably effective.
Among the most studied gut-supportive peptides are:
- BPC-157, derived from a natural protein found in gastric juice, promotes repair of the intestinal lining and supports blood vessel growth in damaged tissues.
- KPV, a fragment of the hormone alpha-MSH, helps calm cytokine-driven inflammation and supports immune tolerance in the gut.
- GHK-Cu, a copper-binding peptide, enhances tissue regeneration and antioxidant defenses throughout the body.
- Larazotide acetate, a tight-junction modulator, helps reduce intestinal permeability and has been researched in celiac disease.
When used as part of a holistic plan that includes whole-food nutrition, stress reduction, adequate sleep, and microbial diversity, peptides offer a biologically natural boost to the body’s own repair process, helping restore the gut barrier from the inside out.
Functional Medicine Support for Gut Repair
At Nourish Medicine, my Austin-based functional medicine practice, we use advanced stool, serum, and metabolomic testing to pinpoint what’s driving your gut dysfunction, whether dysbiosis, infection, inflammation, or low butyrate production, and design precise, root-cause solutions.
If you live in Texas, you can become a patient for individualized care.
If you’re outside Texas, Nourish360 Coaching helps you apply these same healing principles through structured nutrition, lifestyle, and mindset support.
Healing the Whole Self
Your gut is where your body meets the outside world. When that barrier heals, everything improves including your energy, hormones, mood, skin, and immunity.
For a deeper look at whole-person healing, read my book Bloom: 7 Steps to Reclaim Your Health, Cultivate Your Desires, and Reignite Your Spark. It’s a guide to nourishing body, mind, and spirit for lasting wellness
Frequently Asked Questions About Healing Leaky Gut Naturally
How long does it take to heal leaky gut naturally?
Most people feel better within 3–6 weeks; full barrier restoration can take 3–6 months depending on stress, toxins, and inflammation.
What foods help repair the gut lining?
Bone broth, colorful vegetables, polyphenol-rich fruits, omega-3 fats, and fermented foods provide key nutrients and support butyrate production.
Are peptides safe?
When prescribed by a medical professional and sourced from licensed compounding pharmacies, peptides are generally safe and well-tolerated.
Do I need testing to confirm leaky gut?
Functional tests measuring zonulin, calprotectin, secretory IgA, and LPS antibodies reveal permeability and inflammation, guiding personalized care.
About Dr. Alejandra Carrasco, M.D.
Dr. Alex Carrasco is a board-certified family and functional medicine physician, bestselling author of Bloom, and founder of Nourish Medicine in Austin, Texas. She helps patients restore energy, balance hormones, improve gut health, and resolve chronic symptoms through personalized, root-cause strategies that honor the whole person.
Through her practice and Nourish360 Coaching, Dr. Carrasco empowers patients to heal from the inside out and thrive in body, mind, and spirit. Her mission is to combine the best of modern medicine and integrative science to help people reclaim vibrant, sustainable health.
