Leaky Gut and Hormonal Health: How to Heal Naturally with a Naturopathic Approach

Many people know the gut is central to digestion, but what’s less understood is how deeply it impacts hormones. Research and clinical experience now show that leaky gut syndrome — also called increased intestinal permeability — can fuel hormonal imbalances, infertility, thyroid dysfunction, and conditions like PCOS. 

As a naturopathic doctor specializing in hormone health and fertility, I see this gut–hormone connection every day. The good news? Once you understand the link, you can begin to heal leaky gut naturally and restore balance to your hormones.

In this post, we’ll explore:

• What leaky gut is

• The connection between leaky gut and hormones

• Symptoms and causes of leaky gut

• Naturopathic treatments to repair gut lining and balance hormones

What Is Leaky Gut?

Your intestinal lining is meant to be a protective barrier. It selectively allows in nutrients while blocking harmful substances like toxins, bacteria, and undigested food.

This barrier is held together by “tight junctions.” When those junctions loosen due to stress, inflammation, or diet, the gut becomes more permeable — in other words, leaky. Substances leak into the bloodstream, triggering the immune system and setting off inflammation that can disrupt hormones.

Want to learn more about leaky gut? Check out this blog post.

How Leaky Gut Affects Hormonal Health

The gut–hormone connection is complex but powerful. Here’s how leaky gut contributes to hormonal imbalance:

1. Estrogen Metabolism (The Estrobolome Connection)

The gut microbiome contains bacteria that regulate estrogen metabolism. When leaky gut and dysbiosis are present, estrogen recycling gets disrupted:

• Too much estrogen reabsorbed → estrogen dominance → PMS, endometriosis, fibroids, heavy periods.

• Too little estrogen recycling → irregular cycles, hot flashes, fertility struggles.

2. Cortisol and Stress Hormones

Leaky gut creates chronic inflammation, which tells your adrenal glands to pump out cortisol. Over time, this stress response leads to adrenal fatigue and hormone imbalances like:

• Low progesterone (PMS, anxiety, infertility)

• Poor sleep and mid-day crashes

• Blood sugar swings

3. Thyroid Function

About 20% of thyroid hormone conversion happens in the gut. With leaky gut:

• Conversion of inactive T4 to active T3 slows down → fatigue, hair loss, low metabolism.

• Inflammation increases autoimmune risk, especially Hashimoto’s thyroiditis.

4. Insulin Resistance and PCOS

Gut inflammation promotes insulin resistance, which is central to PCOS (polycystic ovary syndrome). That being said, insulin resistance or poorly regulated blood sugar can impact hormones across the board, even in the absence of PCOS. Symptoms may include irregular cycles, acne, hair growth, and difficulty losing weight. Healing leaky gut improves insulin sensitivity and supports metabolic health.

5. Fertility and Pregnancy

Because estrogen, progesterone, cortisol, and thyroid hormones all influence fertility, a leaky gut can reduce conception chances. Gut inflammation is also linked to miscarriage risk and pregnancy complications. For couples trying to conceive, gut healing is a powerful fertility tool.

Signs and Symptoms of Leaky Gut

Wondering if leaky gut might be impacting your hormones? Common symptoms include:

• Digestive issues (bloating, constipation, diarrhea, gas)

• Food sensitivities or reactions

• Brain fog and fatigue

• Skin issues (acne, eczema, psoriasis)

• Autoimmune conditions

• PMS, irregular cycles, PCOS, infertility

If several of these resonate, it may be time to explore naturopathic support for gut healing.

Causes of Leaky Gut

The gut lining is sensitive and can be damaged by:

• Diets high in processed foods, sugar, alcohol

• Chronic stress and high cortisol

• Antibiotics, NSAIDs, and acid-blocking medications

• Gut infections or dysbiosis (imbalanced gut bacteria)

• Food intolerances, especially gluten and dairy

• Toxin exposure (pesticides, mold, heavy metals)

Naturopathic Approach for Leaky Gut and Hormone Balance

From a naturopathic perspective, gut healing protocols focus on removing irritants, reducing inflammation, repairing the lining, and supporting healthy microbes.

1. Remove Gut Irritants

• Try an elimination diet to identify triggers

• Reduce alcohol, sugar, processed foods

• Minimize unnecessary NSAID use

2. Repair the Gut Lining

Nutrients that help heal leaky gut naturally include:

• L-glutamine (fuel for intestinal cells)

• Zinc carnosine (tissue repair)

• Collagen or bone broth (gut lining support)

• Omega-3 fatty acids (anti-inflammatory)

3. Restore the Microbiome

• Probiotic supplements (strain-specific support)

• Fermented foods like kimchi, sauerkraut, kefir

• Prebiotic fibers from garlic, onions, asparagus, green bananas.

• Fiber: Fiber is food for our microbiome. Click here to read more about dietary fiber.

A healthy microbiome helps balance estrogen metabolism and reduces inflammation. With one caveat! Not everyone needs probiotics. Folks with histamine intolerance and folks with certain types of “dysbiosis” or bacterial overgrowth can actually flare with probiotics. 

4. Reduce Stress and Cortisol

Stress management is vital to both gut and hormone health. Techniques like breathwork, yoga, meditation, and walking in nature lower cortisol and support gut barrier repair.

5. Use Healing Botanicals

Herbal medicine can soothe the gut and fight inflammation:

• Slippery elm, marshmallow root, DGL licorice (soothe the lining)

• Turmeric, ginger (anti-inflammatory)

• Berberine or oregano oil (target microbial overgrowths)

6. Support Detoxification and Lifestyle

• Prioritize 7–9 hours of sleep

• Hydrate and eat liver-supportive foods (beets, cruciferous veggies)

• Incorporate daily movement for blood sugar and digestion

Healing Timeline

Most people notice improvements in energy, digestion, and hormonal symptoms within 4–8 weeks of a naturopathic leaky gut protocol. But full gut lining repair and hormone rebalancing often takes several months of consistent effort.

Final Thoughts

The gut is the foundation of hormone balance. If you’ve been struggling with PMS, PCOS, thyroid issues, infertility, or adrenal fatigue, your symptoms may trace back to leaky gut and hormonal imbalance.

The encouraging part? The gut is highly resilient. With naturopathic treatments — including nutrition, lifestyle, and targeted supplements — you can heal leaky gut naturally and reclaim your hormonal health.

If you suspect leaky gut is disrupting your hormones, I’d love to support you. My naturopathic hormone programs are designed to heal from the root, balancing gut and hormone health together. Schedule a consultation here to get started on your healing journey.

Dr. Nicole Kearney is a naturopathic doctor who lives in Burlington, Vermont. She sees patients at her office in Burlington as well as clients nationwide via telehealth. She specializes in fertility, hormonal, thyroid, and gut health.