Ah, perimenopause—the magical time when your hormones throw a party but forgot to invite your gut! Suddenly, your once-happy digestion turns into a rollercoaster ride of bloating, gas, and other ‘surprises’ you never signed up for. If your 40s have brought you more digestive drama than you’d care to admit, don’t worry—you’re not alone. Let’s dive into why your gut health in perimenopause feels like it’s gone rogue and, more importantly, what you can do to get it back on track!

The Main Functions of Our GI Tract
Our GI tract is fascinating. We are still learning so much more about its function and capabilities. Here are the main functions of our GI tract:
- Nutrient absorption. This is obvious but as you will see later on in this blog post, if our gut is not functioning properly our bodies ability to absorb nutrients can become altered.
- Hormone and neurotransmitter production and regulation. Many hormones in the body affect GI function including estrogen, thyroid hormone and serotonin. Did you know that 95% of our body’s serotonin is produced in the GI tract? I find that fascinating. And it really emphasizes the effect that our mood and mental state have on our gut.
- Management of estrogen levels. There is a specific group of microbes in the GI tract that work specifically to metabolize excess estrogen in the body. This is called the estrobolome (again another thing I was not taught in medical training). If your estrobolome is not functioning properly this can lead to an imbalance of estrogen in your body.
- Emotional well-being and mood. There exists a connection between the gut and brain called the gut-brain axis. They are in constant communication. And as discussed above, most of our body’s serotonin is produced in the gut. Low levels of serotonin are associated with increased symptoms of anxiety and depression.
- Support of our immune system. 60-80 percent of our immune system is contained in our GI tract. Thus, if your gut health is impaired, you may have issues with recurrent infections or illnesses and increase your risk for autoimmune diseases.
The Connection Between Hormones and Gut Health
Let’s talk first about how our hormones affect our gut and how the changes that occur with our hormones in menopause impact our digestion and overall gut health. To put this into perspective, the cells that line your entire gastrointestinal tract have receptors for both estrogen and progesterone. This is something that surprised me as I was never taught this in my medical training.
No wonder why so many women experience constipation, bloating, or loose stools before or during their periods! That is one of the many reasons when these hormone levels become erratic in perimenopause, and then eventually decrease with menopause, you may experience unpredictable changes in your bowel patterns and more gas, constipation, and bloating.
But this is only one element of the connection between your gut and hormones. Other hormonal imbalances affect gut function, too. Thyroid imbalances, cortisol dysregulation, or insulin shifts can all influence gut function. And the whole relationship is a two-way street, because your gut is also involved in hormone production and metabolism. This means that your hormone health is directly affected by your gut health.
Hormonal Fluctuations in Perimenopause
Estrogen
During perimenopause, estrogen levels begin to fluctuate and eventually decline. Estrogen plays a significant role in maintaining the gut barrier, which helps protect our digestive system from harmful bacteria. As estrogen levels drop, this protective barrier can weaken, making the gut more vulnerable to inflammation and irritation.
Progesterone
Progesterone, another key hormone, also declines during perimenopause. One of its lesser-known roles is supporting smooth muscle relaxation, including the muscles in the digestive tract. As progesterone decreases, the muscles of the digestive system can slow down, leading to constipation and/or bloating.
Cortisol
Stress tends to increase during perimenopause due to hormonal imbalances, and cortisol—the stress hormone—can spike. When our cortisol levels stay high for long periods of time, this can disrupt our digestion by increasing gut permeability (often called “leaky gut”) and altering the balance of gut bacteria, making it harder for our body to absorb nutrients properly.

How These Hormonal Changes Affect the Gut
Slower Digestion
When progesterone levels drop, the digestive muscles can become less efficient at moving food through the intestines. This can lead to common complaints like bloating, constipation, and a feeling of sluggish digestion. Food stays in the digestive tract longer, which can cause discomfort and interfere with nutrient absorption.
Altered Gut Microbiome
Estrogen has a direct effect on the composition of our microbiome. The microbiome is the community of bacteria that live in our GI tract. As estrogen fluctuates, the balance of beneficial bacteria in the gut may shift, reducing microbial diversity. This imbalance can result in digestive issues like gas, bloating, and even increased susceptibility to gastrointestinal infections. An altered gut microbiome can also affect mood and overall well-being, as the gut-brain connection becomes disrupted.
Increased Inflammation
Declining estrogen levels can increase inflammation in the gut, making it more sensitive and reactive. This might lead to symptoms such as bloating, gas, or discomfort after eating certain foods. The weakening of the gut barrier also allows more harmful bacteria to pass through, which triggers the immune system and can result in chronic low-grade inflammation.
In perimenopause, these hormonal fluctuations create a perfect storm for digestive disruption. However, by understanding these changes, we can take steps to support our gut health and alleviate uncomfortable symptoms.
Common Gut Issues in Perimenopause
As discussed above, hormonal fluctuations can often lead to digestive changes that can cause discomfort and disrupt our daily life. Let’s break down the most common gut issues during perimenopause
Bloating, Gas, and Constipation
Bloating
Many women notice that their abdomen feels fuller or more swollen during perimenopause, even after eating a normal-sized meal. This bloating can result from hormonal changes slowing digestion, which causes food to stay in the gut longer and ferment, leading to gas buildup.
Gas
With slower digestion, undigested food can ferment in the colon, producing excess gas. Changes in the gut microbiome due to fluctuating estrogen levels can also contribute to increased gas production, causing discomfort and embarrassing situations.
Constipation
Progesterone, which helps regulate muscle contractions in the intestines, decreases during perimenopause. As a result, intestinal motility slows down, leading to constipation. This can make it difficult to have regular bowel movements, causing discomfort and bloating. Dehydration or reduced fiber intake can worsen this problem, as can stress.
Changes in Bowel Movements and Digestive Discomfort
Irregular Bowel Movements
Hormonal shifts during perimenopause can lead to inconsistent bowel patterns, ranging from constipation to diarrhea. Some women experience alternating episodes of both, which can be confusing and disruptive to their daily routines. The decreased efficiency of the digestive muscles, along with inflammation caused by estrogen decline, may contribute to this unpredictability.
Digestive Discomfort
Alongside bloating and gas, we may experience general digestive discomfort such as cramps, nausea, or a sense of fullness after eating. These issues often stem from slower digestion and changes in the gut microbiome, which can make it harder for the body to break down certain foods effectively. Perimenopause also triggers food sensitivities or intolerances that previously didn’t exist, exacerbating gut discomfort.
The Role of Stress and Its Effect on the Gut-Brain Axis
Stress Amplifies Gut Issues
Stress levels can skyrocket during perimenopause due to life changes, sleep disruptions, and hormonal imbalances. This increase in stress triggers the release of cortisol, the stress hormone, which can negatively affect gut function. Chronic stress causes the digestive system to go into “fight or flight” mode, slowing down digestion and making the gut more prone to inflammation.
The Gut-Brain Axis
The gut and brain are closely connected through the gut-brain axis, a two-way communication system where emotions and stress can directly impact gut health. In perimenopause, this connection becomes more pronounced as fluctuating hormones and heightened stress influence the nervous system. Stress can alter gut motility (leading to constipation or diarrhea) and exacerbate conditions like irritable bowel syndrome (IBS), while digestive discomfort can in turn worsen mood and anxiety levels.
Gut Health and Mood
The gut produces many neurotransmitters, such as serotonin, which influence mood. When the gut is imbalanced due to stress or hormonal changes, serotonin production may drop, affecting mental well-being. This creates a vicious cycle where stress impacts digestion, and poor digestion worsens stress and mood.
In summary, perimenopause often brings digestive challenges like bloating, gas, constipation, and irregular bowel movements, driven by hormonal changes. Stress plays a huge role, affecting the gut-brain axis and amplifying these issues. However, by managing stress and being mindful of diet and lifestyle changes, we can help reduce these gut problems during perimenopause.
The Importance of Diversity in Our Microbiome
Here is a fun fact:
You have 10 times as many bacteria in your body than you do cells in your body! Most of these bacteria live in your digestive tract.
There are over 100 trillion bacteria in the gut. These include both good and bad bacteria. This collection of bacteria is referred to as the gut microbiome. Some of these bacteria, such as E. Coli, can cause disease. However, most of the bacteria in your gut are beneficial. These bacteria don’t just sit around and do nothing. They help to absorb and digest nutrients and provide immunity from unwanted pathogens.

Foods That Support Gut Health in Perimenopause
Your diet has the greatest impact on your gut flora. As hormonal fluctuations in perimenopause affect digestion and the gut microbiome, focusing on gut-friendly foods becomes essential. Here’s how specific food choices can help:
Fiber-Rich Foods (Fruits, Vegetables, Whole Grains)
Fiber is key to maintaining healthy digestion, especially during perimenopause when constipation and sluggish digestion are common. If I could only do one thing to help my gut health it would be to make sure I am eating enough fiber. Fiber adds bulk to stools, promoting regular bowel movements, and helps prevent bloating and gas by keeping the digestive system running smoothly.
There are two different types of fiber found in foods. Both have different benefits and are equally important.
Soluble fiber
Soluble fiber is found in oats, apples, and beans. It is called soluble fiber because it dissolves in water and forms a gel-like substance that helps slow digestion and regulate blood sugar.
Insoluble fiber
Insoluble fiber is found in whole grains, nuts, and vegetables. It is not soluble in water and adds bulk to the stool, helping food move through the digestive tract more efficiently.
Examples of Fiber-Rich Foods
Fruits: Berries, apples, pears, and citrus fruits.
Vegetables: Leafy greens (spinach, kale), broccoli, and carrots.
Whole Grains: Quinoa, brown rice, oats, and barley.
Beans and legumes.
You should aim to eat at least 25 grams of fiber each day and try to get that fiber from a variety of foods. Eating a vegan (plant-based) diet makes that pretty easy and is one of the many benefits.

Prebiotics and Probiotics
Prebiotics
These are non-digestible fibers that feed the good bacteria in your gut, helping to maintain a healthy balance of the microbiome. Prebiotics act as “fertilizer” for the beneficial bacteria and are found in foods like garlic, onions, bananas, and asparagus.
Probiotics
These are live beneficial bacteria that can help restore gut balance, especially during perimenopause when hormonal shifts disrupt the microbiome. Probiotics are found in fermented foods like sauerkraut, kimchi, kombucha, and plant-based yogurts with live cultures.
Why They Matter
Eating a mix of prebiotic and probiotic foods helps foster a balanced gut microbiome, which improves digestion, boosts immunity, and even positively affects mood.
Hydration and Its Role in Digestion
Staying well-hydrated is essential for digestion because water helps break down food and aids in the absorption of nutrients. It also helps prevent constipation by softening stools, making them easier to pass.
As progesterone levels decline, constipation can become more frequent. Drinking enough water keeps the digestive system moving and helps to offset the effects of sluggish digestion. A good rule of thumb is to aim for at least 8 glasses of water a day, but this can vary depending on individual needs and activity levels. The easiest way to know if you are hydrated is to look at your urine. I know, gross but hear me out. If your urine is dark yellow, you probably need to drink more water and if it is close to clear in color you are probably overhydrated.
Lifestyle Changes for a Healthy Gut
In addition to diet, certain lifestyle factors can significantly impact gut health, especially during the hormonal changes of perimenopause.
Regular Physical Activity and Its Impact on Gut Motility
Exercise Boosts Digestion
Physical activity stimulates the muscles in the intestines, helping to move food through the digestive tract more efficiently. This can alleviate common issues like bloating and constipation.
What Exercises are the Best?
Any regular movement, even in the form of walking or light strength training, can promote gut motility. Activities like yoga can also be especially helpful as it encourages relaxation and reduces bloating.
The Gut-Exercise Connection
Studies show that consistent exercise promotes a healthier gut microbiome, reduces inflammation and supports overall gut health. Even moderate activities can have a significant positive impact.
Stress Management Techniques
Stress and Digestion
Stress, particularly chronic stress, has a direct impact on the gut due to the gut-brain axis. High cortisol levels from stress can slow down digestion, exacerbate symptoms like bloating and constipation, and alter the gut microbiome, leading to digestive discomfort.
Effective Stress Management Tools
Meditation: Helps calm the nervous system, reducing cortisol levels and easing digestive stress.
Yoga: Combines movement and breathwork to reduce stress, enhance gut motility, and improve overall digestion.
Deep Breathing: Engaging in regular deep breathing exercises can stimulate the vagus nerve, which plays a key role in gut health by helping regulate digestion.
Managing stress is crucial during perimenopause, as stress hormones can exacerbate gut issues. By incorporating stress-reduction techniques, women can improve their digestive health and overall well-being.
How Sleep Quality Affects Digestion and Gut Health
The Sleep-Digestion Link
Poor sleep can negatively impact gut health by disrupting the body’s natural circadian rhythms, which play a role in digestion. Without proper rest, the digestive system becomes sluggish, leading to constipation, bloating, and other gastrointestinal issues.
Sleep and the Microbiome
Lack of sleep can also affect the balance of the gut microbiome, leading to reduced diversity and an increase in harmful bacteria. This can make the gut more prone to inflammation and negatively affect digestion.
Improving Sleep for Better Gut Health
Establishing a regular sleep routine, limiting screen time before bed, and creating a restful environment can help improve both sleep quality and digestion. Getting 7-9 hours of sleep per night allows the digestive system to rest and repair, promoting healthier gut function.
By focusing on gut-friendly foods and making mindful lifestyle changes, we can maintain better digestion and overall gut health, despite the challenges posed by hormonal fluctuations.
Supplements to Consider
I will be real with you here, the best way to help your gut is to eat a high fiber diet, consume probiotic foods, exercise regularly and manage your stress. I do not think that supplements are all that beneficial and that our money can be better spent on other things.
That being said, if you are following the recommendations above and still struggling, I would recommend you first seek the help of a licensed healthcare professional to make sure there is not anything else going on that could be causing your symptoms. You can also consider trying the following supplements.
Probiotics
There are a lot of different options on the market and most of them suck. Many of the probiotic supplements out there are not effective as the bacteria in them never make further down into your GI tract where they are needed. It is important to consider this and buy from a reputable company. Some things to consider are the types of strains in the supplement. Certain probiotic strains may be more beneficial during perimenopause. Lactobacillus and Bifidobacterium strains have shown promise in supporting hormone balance and digestive health. It is important to make sure that the supplement has multiple strains to help ensure a diverse gut flora.
If you are looking for more information on gut health and probiotic supplements, then check out this guide developed by Dr. Will Bulsiewicz a trusted gastroenterologist.
Dr. Bulsiewicz Probiotic Guide
Digestive enzymes
I’ve noticed a lot of protein powders contain these. Not sure if they are beneficial or not. As we discussed above, hormonal changes can affect the production of digestive enzymes. So, in theory if you are having issues with symptoms of indigestion like bloating or gas after meals, difficulty digesting fatty foods or feelings of fullness or discomfort after eating then taking a digestive supplement with a meal may help.
Magnesium for constipation
Magnesium helps to relax muscles, including our digestive muscles. It also helps to draw more water into the intestines which helps to soften our stool. There are many different types of magnesium supplements out there but those containing magnesium citrate and/or magnesium oxide are more beneficial in relieving constipation. I have used this supplement in the past with good results: Natural Calm. It is important to note that taking too much may have the opposite effect (diarrhea, abdominal cramping).

When to Seek Professional Help
Any new symptom or change in your bowel habits would benefit from a consultation with a professional to rule out anything serious. If you are 45 and older, get a screening colonoscopy. I had one this year and it was not a big deal at all.
Red flags to watch for (any of these symptoms require a medical evaluation ASAP)
- Persistent abdominal pain lasting more than a few days
- Unexplained weight loss (e.g., 5% or more of body weight in 6-12 months without trying)
- Severe or chronic diarrhea or constipation
- Blood in stool or black, tarry stools
- Persistent heartburn or acid reflux not relieved by over-the-counter medications
- Difficulty swallowing
- Nausea or vomiting that doesn’t subside
- Any significant change in bowel habits that persists for more than a few weeks
I don’t mean to scare anyone, but it is important to note that while gut health issues are common during perimenopause, they shouldn’t be ignored or considered “normal.” You need to be proactive about your digestive health and seek professional help when needed.
Conclusion
Our GI tract is so much more than a tube that digests our food. Everyone needs to live a life that supports their gut health, especially women in perimenopause. The best ways to achieve this is through a high fiber diet (25-35 grams per day), regular exercise, probiotic foods and stress management.
Here are some gut friendly recipes to help you meet your fiber needs and include more probiotics into your diet:
How to Make Soy Yogurt in the Instant Pot
High Protein Wrap with Tofu and Veggies
If you would like more information on diet and exercise, specifically how to increase muscle and burn fat in menopause, then check out the guide below. It is a FREE document that provides you with a detailed plan.