How gut health affects hormones and your menstrual cycle

Your gut isn’t just for digesting food; it’s a powerhouse that influences nearly every system in your body, including your hormonal health. Often referred to as the "second brain," your gut microbiome plays a pivotal role in regulating mood, immunity, and even your menstrual cycle. For women, gut health can have a profound effect on hormonal balance, especially in conditions like PCOS (Polycystic Ovary Syndrome) and menstrual irregularities.
In this article, we explore the connection between gut health and hormones, their impact on your menstrual cycle, and the steps you can take to support both of them naturally.
Understanding the gut-hormone connection
The gut microbiome is home to trillions of bacteria that help regulate key bodily functions, including hormone metabolism.
Hormone metabolism and regulation
The gut plays a crucial role in metabolising and recycling hormones, including oestrogen and progesterone, two female sex hormones. A group of gut bacteria known as the estrobolome plays a specific role in processing oestrogen. When gut bacteria are imbalanced, it can lead to excess oestrogen circulating in the body, contributing to symptoms like bloating, mood swings, and irregular periods.
The gut-liver axis
The liver works closely with the gut to detoxify and clear hormones from the body. When the gut microbiome is out of balance, it may affect how efficiently the liver clears hormones, especially oestrogen. This can contribute to oestrogen dominance, which is linked to PMS (Premenstrual syndrome), heavy periods, and fibroids.
The gut-brain axis
The gut communicates with the brain through the vagus nerve, influencing the release of hormones like cortisol and serotonin [1]. Cortisol, the stress hormone, can directly affect menstrual cycle regularity, while serotonin is essential for mood stability, explaining why gut imbalances can also trigger emotional PMS symptoms.
The effect of gut health on the menstrual cycle
Imbalances in the gut, like dysbiosis (an overgrowth of harmful bacteria) or leaky gut, where bacteria and toxins can enter the blood steam from the intestine, can throw your hormones off balance, which inevitably disrupts your menstrual cycle. Find out more about these imbalances and how they can impact your menstrual cycle.
Gut imbalances and irregular cycles
Dysbiosis can impair hormone regulation, leading to irregular ovulation or anovulatory cycles [2] (where the egg is not released from the ovary). A compromised gut lining (leaky gut) may also allow toxins into the bloodstream, increasing systemic inflammation, which negatively impacts hormone function.
PMS, Cramping, and Mood Swings
Poor gut health is often associated with increased inflammation, which may worsen PMS symptoms like cramping, breast tenderness, and mood instability. When gut bacteria aren't producing enough short-chain fatty acids (SCFAs), which reduce inflammation, PMS symptoms can become more severe.
Digestion and Hormonal Excretion
Slow digestion or chronic constipation can delay hormones from being excreted from the body, causing oestrogen to recirculate back around the bloodstream. This can cause an excess of oestrogen in the body. Supporting digestion through diet and adequate hydration is essential to maintaining hormonal balance. Regular bowel movements = better hormone balance!
PCOS and gut health: What’s the link?
PCOS affects up to 10% of women of reproductive age [3] and is characterised by hormonal imbalances, insulin resistance, and irregular periods. Emerging research shows a strong link between PCOS and gut health [4].
Gut microbiota and PCOS
Women with PCOS often have reduced diversity in gut bacteria, which can lead to insulin sensitivity and increase inflammation. A disrupted microbiome may cause symptoms such as weight gain, acne, and menstrual cycle irregularities.
Insulin sensitivity and hormones
Improving gut health may support better insulin regulation, which is essential for keeping blood sugar levels stable. Insulin is a hormone that helps move glucose from your bloodstream into your cells, providing your body with energy. When your body becomes resistant to insulin, blood sugar levels can remain high, which can disrupt overall hormonal balance.
For individuals with PCOS, insulin resistance is common and can contribute to increased production of androgens (a group of sex hormones that include testosterone). Higher levels of androgens can interfere with regular ovulation and menstrual cycle patterns, leading to symptoms like irregular periods, acne, and excess hair growth. By supporting your gut health, you may improve insulin sensitivity, helping to stabilise blood sugar levels and reduce excess androgen production, which in turn may support more regular ovulation and menstrual health.
Natural gut healing for PCOS
A gut-friendly diet high in fibre, antioxidants, and fermented foods like kimchi and kefir can support hormonal balance. Probiotics may also help restore microbial diversity and reduce inflammation, improving PCOS symptoms naturally.
Signs your gut may be affecting your hormones
Not sure if your gut is to blame for hormonal issues? Here are some common red flags:
- Persistent bloating or gas
- Irregular menstrual cycles
- Mood swings or heightened PMS
- Fatigue or brain fog
- Sugar cravings or weight fluctuations
These signs often point to underlying gut issues that may be disrupting your hormone levels.
Supporting gut health for hormonal balance
Taking care of your gut is one of the most effective ways to improve your hormonal health. Here’s how:
Eat for your microbiome
- High-fibre foods like oats, lentils, flaxseeds, and vegetables support digestion and hormonal clearance.
- Fermented foods like kimchi, sauerkraut, and yoghurt replenish healthy bacteria.
- Prebiotic-rich foods such as garlic, onions, and bananas feed beneficial microbes.
You can learn more about what foods are good for your gut with our guide on the best food for your gut (and what to avoid).
Probiotics and Supplements
If you can’t incorporate enough probiotics into your diet, probiotic supplements can help restore gut balance [5], especially strains like Lactobacillus and Bifidobacterium. Omega-3 fatty acids, magnesium, and zinc can also support hormonal harmony and reduce inflammation.
Lifestyle habits
- Sleep: Aim for 7–9 hours to allow your body to rest and repair.
- Exercise: Regular movement enhances gut motility and also lowers cortisol!
- Stress management: Chronic stress damages the gut lining and increases hormone-disrupting cortisol levels. Try meditation, journaling, or breathwork.
When to Seek Help: Working with a Health Professional
If you’re dealing with persistent gut or hormonal symptoms that don’t improve with lifestyle changes, it may be time to work with a specialist.
They can help:
- Identify root causes of hormonal imbalances
- Recommend personalised treatment plans
- Run tests to evaluate gut microbiome diversity and inflammation markers
Did you know that Smart Salem offers a comprehensive Gut Microbiome Health Test to help you get to the bottom of your symptoms and take actionable steps toward better health?
Conclusion: Why supporting your gut is key to hormonal health
Your gut is the unsung hero of hormonal health. From regulating oestrogen levels to influencing mood and menstrual cycle regularity, your microbiome plays a central role in how balanced and healthy you feel. Whether you’re managing PCOS, struggling with PMS, or simply want more regular periods, focusing on gut health can make a profound difference.
Start with simple steps, clean up your diet, manage stress, prioritise sleep, and if needed, seek professional support. Your hormones will thank you.
FAQs
Can poor gut health really affect my menstrual cycle?
Yes. An imbalanced gut can disrupt hormone metabolism, increasing the risk of irregular periods, PMS, and hormonal acne.
What are the signs that my hormones and gut health are connected?
Common symptoms include bloating, fatigue, mood swings, irregular periods, and digestive issues.
Can improving gut health help with PCOS symptoms?
Absolutely. A healthy gut can improve insulin sensitivity, reduce inflammation, and support hormonal balance—all key to managing PCOS.
What foods are best for balancing gut health and hormones?
Fibre-rich vegetables, fermented foods, and prebiotics are excellent foods to incorporate for better gut and hormonal health. Avoid processed sugar and inflammatory oils like sunflower oil.
Do probiotics help with hormonal balance?
Yes, probiotics can support the gut microbiome, aiding hormone regulation and reducing inflammation that affects hormonal balance.