Gut Check: How SIBO Can Wreck Your Hormones and What to Do About It

Dr. Jen
Jun 30
4 min read

Do you feel like your hormones are hijacking your life—despite eating clean, trying supplements, or even taking hormone therapy?

You’re bloated after every meal. Your moods swing unpredictably. Your periods are irregular or intense. You’re exhausted, foggy, and can’t lose the extra weight, no matter how hard you try.

And yet… your labs keep coming back “normal.”

Let me tell you what many doctors miss:

Your hormone chaos may not be hormonal in origin. It could be coming from your gut.

More specifically—from SIBO (Small Intestinal Bacterial Overgrowth), a silent disruptor affecting millions of women, often without a clear diagnosis.

SIBO doesn’t just cause digestive issues. It triggers a systemic chain reaction that disrupts liver detox, thyroid conversion, adrenal balance, insulin sensitivity, and estrogen metabolism.

Translation? It wrecks your hormones at every level.

In this blog, I’ll walk you through exactly how SIBO sabotages your hormonal health—from estrogen overload and thyroid slowdowns to cortisol crashes and PCOS-like symptoms.

Because if you’ve been stuck in a hormonal spiral with no clear answers, your gut may be the missing piece.

What is SIBO?

SIBO stands for Small Intestinal Bacterial Overgrowth. It occurs when bacteria that normally thrive in the large intestine migrate and multiply in the small intestine—where they don’t belong.

These bacteria ferment your food (especially carbs and fiber) too early in the digestive process, releasing gas and toxins that trigger:

Abdominal bloating and distension
Constipation, diarrhea, or mixed IBS
Belching, nausea, or reflux
Nutrient malabsorption
Chronic inflammation

And beyond these gut symptoms, SIBO wreaks havoc on your hormones.

But here’s what many women don’t realize:SIBO can silently sabotage your hormone health.

4 Ways SIBO Disrupts Hormones in Women

Your hormones don’t work in isolation—they depend on healthy gut, liver, immune, and detox systems to stay balanced. When SIBO throws those systems into chaos, hormone imbalance is inevitable.

Here’s how SIBO triggers hormone mayhem in women:

1. Estrogen Dominance & Detox Failure

Your liver and gut are the main detox channels for estrogen metabolism. When SIBO fuels dysbiosis (an imbalanced microbiome), it alters the estrobolome—the bacterial genes that metabolize estrogen. This means:

Estrogen gets recirculated instead of excreted
Estrogen metabolites become more inflammatory and harmful
You may experience heavy periods, breast tenderness, irritability, water retention, or fibroids

2. Thyroid Dysfunction (Even When Labs Look Normal)

The gut-thyroid axis is real. Inflammation from SIBO:

Reduces T4 to T3 conversion
Lowers gut absorption of selenium and iodine
May trigger Hashimoto’s via leaky gut and molecular mimicry

This can lead to fatigue, cold hands and feet, constipation, hair thinning, and weight gain—even if your TSH looks “normal.”

3. Adrenal Burnout & Cortisol Chaos

SIBO is a chronic stressor. It activates the HPA axis (your brain-adrenal communication system) and triggers constant low-grade inflammation. Over time, this leads to:

Elevated cortisol → anxiety, insomnia, belly fat
Cortisol crashes → fatigue, brain fog, low resilience to stress
Disrupted DHEA, progesterone, and testosterone production

This means you’re wired and tired—and stuck in a hormone-depleting stress loop.

4. Insulin Resistance & PCOS Risk

SIBO bacteria thrive on sugar—and drive your cravings for it. This creates blood sugar spikes and crashes that:

Impair insulin sensitivity
Increase visceral fat
Drive androgen excess and irregular ovulation
Worsen PCOS-like symptoms (acne, oily skin, facial hair, weight gain)

Signs SIBO Might Be Behind Your Hormone Symptoms

If any of the following sound familiar, it’s time to look at your gut—not just your hormones:

You bloat after eating almost anything
You have cyclical anxiety, PMS, or mood swings
Your periods are heavy, irregular, or painful
You’re tired no matter how much you sleep
You’re stuck in a plateau despite clean eating
You’ve been told “your labs look fine” but still feel off

Diagnosing SIBO: It’s Not All in Your Head

The gold standard for SIBO testing is a lactulose or glucose breath test, which measures hydrogen and methane gas levels. However, I often spot SIBO based on clinical symptoms, food responses, and history—especially when patients have IBS, autoimmunity, or unexplained hormone chaos.

My Root-Cause SIBO Protocol

Conventional antibiotics like rifaximin can help some cases—but I’ve seen far better outcomes using a holistic approach that addresses the whole body.

My signature SIBO protocol includes:

Herbal antimicrobials (like oregano oil, berberine, allicin)
Biofilm disruptors to break down bacterial defense shields
Motility agents like ginger or bitters to keep things moving
Digestive support (enzymes, HCl, ox bile)
Hormone & mitochondrial nutrients (magnesium, B6, NAC, CoQ10)
Faith-based emotional support for stress and nervous system healing

This isn't a one-size-fits-all detox. It's a strategic healing plan customized for women’s unique physiology.

What to Eat: Low-FODMAP, High-Nutrient

While you don’t need to eat low-FODMAP forever, reducing fermentable carbs during SIBO treatment can ease symptoms while healing takes root.

Here’s what that looks like:

❌ Avoid (Temporarily):

High-fructose fruits (apples, mango, watermelon)
Onions, garlic, leeks
Beans and lentils
Cow’s milk dairy
Sugar alcohols (xylitol, sorbitol)

✅ Focus On:

Cooked, low-FODMAP veggies (zucchini, spinach, carrots)
Protein-rich meals (wild fish, pasture-raised eggs, organic chicken)
Gluten-free grains (quinoa, white rice, millet)
Bone broth and gut-soothing herbs
Prayer, rest, and rhythm to support your body’s recovery

What Can You Do?

At Healthy by Dr. Jen, I take a root-cause approach to treating SIBO naturally. My SIBO protocol includes:

Herbal antimicrobials
Biofilm disruptors
Digestive enzymes
Motility support
Mitochondrial + hormone detox nutrients
Food guidance without crash dieting

Women following this plan often report better energy, more regular cycles, clearer skin, and even weight loss—because we’re not just treating symptoms, we’re rebuilding balance.