5 Sneaky Ways Your Gut Messes With Your Hormones

If you’re dealing with PMS that wrecks your week, unpredictable cycles, stubborn weight, acne that laughs at your skincare routine, or anxiety that spikes out of nowhere, there’s a good chance your gut is quietly running the show. And no… that doesn’t mean you just need more probiotics. Your gut is one of the main control centers for how your body processes estrogen, cortisol, insulin, and even thyroid hormones. When it’s off, your hormones don’t stand a chance. I see this constantly in the women I work with here in Utah and Idaho (bare with my SEO keywords, haha)… people doing “all the right things” but still stuck.

First, your gut literally decides whether estrogen gets recycled back into your body or flushed out. Certain gut bacteria produce an enzyme called beta-glucuronidase, which can reactivate estrogen in your intestines and send it right back into circulation. When that system is out of balance, estrogen hangs around longer than it should, which can lead to heavy periods, breast tenderness, endometriosis, fibroids, and mood swings. A 2017 review in Endocrine Reviews confirmed that gut bacteria play a direct role in regulating circulating estrogen levels through what’s called the estrobolome (Plottel & Blaser, 2011; Baker et al., 2017).

Second, inflammation in the gut makes your hormones louder and more chaotic. When the gut lining is irritated or “leaky,” inflammatory compounds get into the bloodstream and tell your adrenal glands to pump out more cortisol. Chronically elevated cortisol doesn’t just make you tired — it suppresses progesterone, worsens PMS, and throws off blood sugar, which then impacts insulin and testosterone. Research in Frontiers in Immunology shows that gut permeability is tightly linked to systemic inflammation and hormone signaling (Camilleri, 2019). Translation: if your digestion is inflamed, your hormones are too.

Third, your gut controls how well you absorb the raw materials for hormone production. Things like magnesium, zinc, B vitamins, and amino acids are literally the building blocks of estrogen, progesterone, and thyroid hormones. If you’re bloated, constipated, or dealing with food sensitivities, you’re probably not absorbing what you eat — even if your diet looks “healthy.” That’s one reason so many women who come to me feel like they’re doing everything right but still show deficiencies on labs.

Fourth, gut bacteria also regulate insulin and blood sugar — which is a huge deal for hormones. Blood sugar spikes drive insulin up, which then pushes testosterone higher and disrupts ovulation. This is one of the main pathways behind PCOS and stubborn belly fat. Studies published in Cell Metabolism show that microbiome diversity directly affects insulin sensitivity and metabolic hormones (Ridaura et al., 2013). So if your gut is off, balancing blood sugar becomes nearly impossible.

And finally, your gut makes neurotransmitters that talk to your hormones. About 90% of your serotonin is made in the gut, and serotonin helps regulate sleep, appetite, and estrogen signaling. Poor gut health = poor sleep, higher cortisol, worse PMS, and more cravings. That’s why so many women notice their cycles fall apart when their digestion does.

The frustrating part? You can’t fix this with random supplements or another 30-day cleanse. You need to know which hormones are off and why — and how your gut is driving that pattern.

👉 Download the Hormones, Explained Guide to see how your gut, blood sugar, and cycle connect — and what actually moves the needle.