Menopause and IBS: What is the Connection?
So many women find that digestive symptoms start or become worse around perimenopause, experiencing uncomfortable constipation, diarrhoea, urgency, bloating, flatulence and other embarrassing symptoms.
Why is that?
More importantly, what can you do about it?
Read on to find out why this time of life can be the start or, worsening of these uncomfortable and embarrassing symptoms, and how natural medicine can help you to feel normal again.
Digestive changes in perimenopause
Some women find they have no digestive issues until they get to about 38-40, then everything seems to change. Others find that previously manageable symptoms get worse around this time. Why is that?
Some terminology first:
Menopause starts 12 months and 1 day after your last menstrual bleed, with the average being around 50-53 years of age
Perimenopause is the 10-12 years before menopause and has 4 stages. Each of these stages marks differing changes in hormone levels.
Estradiol, the main type of estrogen, starts to fluctuate around the start of perimenopause, potentially as early as 12 years before menopause - even as early as 38 or as late as 48! If you’ve had surgery to remove your ovaries or chemotherapy, then likely even earlier (known as surgical menopause).
Estradiol is helpful for many things, one is for keeping our stress hormone cortisol under control. When we are in a stressful situation, excited (good or bad), injured or infected (by a virus or other pathogen), or even intense exercise - our body produces cortisol for protection from inflammation and regulating energy for a quick escape. What is supposed to happen is to return to a calm ‘rest and digest state’ where the cortisol lowers again. With less oestradiol, cortisol increases further, raising blood pressure, increasing blood glucose and slowing digestion. This can trigger or make IBS, SIBO, constipation or diarrhoea worse.
With fluctuating estradiol, our sleep and mood can also be affected, which can also impact our digestive function. We are more likely to feel stressed, tired and moody which can alter:
The production of hydrochloric acid in the stomach - necessary for absorbing nutrients like zinc, magnesium, calcium and iron, digesting proteins and protecting our gut from pathogens we ingest
Production of other gastric secretions for breaking down foods and absorbing nutrients
The types, the makeup and diversity of our gut microbes
The frequency and strength of peristalsis (the muscle contractions that push food through the digestive system) this slowing down can mean more water is absorbed from the stool, causing a firmer stool and contributing to constipation
The migrating motor complex (MMC) - a stronger wave-like contraction that occurs every 90 minutes between meals, which is like a cleaning process. Poor/no MMC function can trigger SIBO (small intestinal bacterial overgrowth), or SIFO (small intestinal fungal overgrowth) as it is required to help control bacteria and fungal growth in the small intestines.
The pH of our gut, our blood and lymphatic fluids
The sensitivity of our gut and how we feel pain or discomfort
Progesterone is the other main hormone which also starts to diminish during perimenopause. Progesterone can impact the way bile is produced in the liver, causing it to be more concentrated. It also helps to relax the muscle contractions of peristalsis, and of the MMC which can result in a greater tendency to constipation in menopause.
The relationship between your gut and your hormones runs deeper than most people realise.
For a comprehensive look at
how your digestive system drives hormonal symptoms,
read my article on
What causes IBS and digestive symptoms?
Digestive symptoms and IBS can be caused by many different factors. Many of these are increased, or we have an increased sensitivity to them either as we age generally, because of the withdrawal of estrogen and progesterone or from other lifestyle factors that happen around the time of perimenopause and menopause. These include:
Food intolerances or allergies
Chronic stress, anxiety, intense over-exercising
Disruption to the types of species, the relative numbers and the abundance of different species of microbiota in the colon
Some species can be in the wrong place in the digestive system e.g. in small intestinal bacterial overgrowth (SIBO), microbes that should be only lower down in the colon, can be found up in the small intestines where there should be very few microbes
Intestinal hyper-permeability (used to be called Leaky Gut), where the cells that line the gut allow large molecules to leak out and trigger food intolerances and allergies
Low hydrochloric acid in the stomach, which can cause all of the above as well as poor nutrient absorption, and poor breakdown of proteins
Structural defects, like scarring, adhesions, diverticula (pockets in the bowel), and poor muscle tone which reduces peristalsis
Disruption to the migrating motor complex - a wavelike motion that occurs every 90 mins or so, (but only between meals) which is like a cleaning process in the gut
Constipation from low fibre diet, or poor hydration
With-holding bowel movements, which can cause water absorption from the stool and lead to constipation
Poor nutrition leading to insufficient hydrochloric acid, enzymes
Excess alcohol consumption
Some medications
Smoking
Parasites, or other infections (viruses, COVID, food poisoning, gastro)
Hormonal fluctuations
If your symptoms include significant bloating, constipation or diarrhoea that has not responded to usual approaches, SIBO may be a contributing factor. Read about SIBO and natural treatment strategies here.
Could it be related to food intolerances?
In a word, yes! And, so often this is the case. There are some really common offenders, but equally, you can be intolerant or allergic to pretty much anything.
Most often, wheat, gluten and dairy cause problems and because they are in SO many foods, and eaten so regularly it can be really difficult to tease this out. You can go your whole life without an issue with wheat or gluten, or dairy and then one day, it’s a problem - because you no longer have the tolerance for it. Your body is now saying ‘no’, and there may or may not have been a trigger for it like a virus or an infection.
In perimenopause and menopause due to the fluctuation and then stopping of both estrogen and progesterone which are protective of the immune system and how it reacts, many women (and AFAB’s) find that they develop gut problems AND they are more allergic to other things as well. Some women find they start experiencing hayfever when they’ve never had it before, or other symptoms of high histamine. This can happen particularly in perimenopause when surges of estrogen can interact with histamine causing food and other allergies.
Developing histamine intolerance is also common, and this will cause gut problems such as diarrhoea, urgency, flatulence, sometimes hives, and often migraines and mood issues. This is another kind of food intolerance and is relatively easy to treat with some dietary changes, and herbal and nutritional support.
Sometimes, this might mean eliminating this food from your diet for a while, or forever, it just depends. Always do this under the guidance of a naturopath or nutritionist because cutting foods out of your diet can mean unnecessary and harmful nutritional deficiencies if not managed properly. Diets like the FODMAP, Keto or Carnivore diet can bring temporary relief but are not healthy long-term. They can disrupt the microbiome due to the lack of specific nutrients required to support beneficial microbes.
Other foods that are common triggers, can be: soy (sometimes just the non-organic), oats, almonds, nuts, fermented foods (yes, they are great if your gut is 100% healthy, but equally can be aggravating), tomatoes, citrus, fish, animal proteins. It is possible to be intolerant to any food, so, sometimes you’ll need some help working out which foods you should avoid, at least for a while.
What testing can I do?
Testing is great, however, it’s often expensive and not always essential. Some practitioners say ‘test, don’t guess’ and others will say ‘nothing beats a good case history’ - I sit firmly on the fence here. A good quality test such as the GI 360 or the Microba can give you a great overview of species diversity and abundance, and the presence of parasites, intestinal hyperpermeability and inflammation, however, they are only ever a snapshot in time. They reflect what is happening in your gut for that particular moment, on that particular day and given the microbiome can change within 4 hours, it might be a more accurate reflection of the last day or so. Having said that, they can provide a great baseline, to see how you biome has changed with treatment. Yes, they are useful, but only as a guide.
A comprehensive case history on the other hand can give so much information, and often all that is needed to be able to treat a condition.
So, if you have the money for testing, great! And, if you don’t then we’ll still take a deep dive into your symptoms, your past medical history, diet, medications, travel, family history and more. Whilst we wait for the results we’ll start a treatment based on your case, symptoms, past history, family tendencies, diet and lifestyle factors.
How does conventional medicine treat IBS?
Conventional medicine treatment for IBS (as prescribed by the RACGP clinical guidelines), might involve diagnosis using the Rome IV criteria and your GP may refer you for investigations to rule out celiac disease, or other conditions. Treatment might include the FODMAP diet, managed via an app such as Monash University IBS app. You may be referred to specialist private IBS clinics where a combination of hypnotherapy and FODMAP diet are provided. You GP may prescribe antidepressants, anti-spasmodics, laxatives or antidiarrheal medications and/or peppermint oil, fibre supplements and probiotics, yoga, and psychologists for CBT (cognitive behavioural therapy) or other treatments to help with anxiety, stress or depression which may be underlying your digestive symptoms.
Often people find that these methods do not adequately address their symptoms, or would prefer not to take pharmaceutical medications long term, or simply require a practitioner who can spend more time understanding the full picture. This is where natural medicine offers something genuinely different.
How natural medicine can help
Complementary and alternative medicine practitioners have understood the relationship between gut health and whole-body wellbeing for centuries. Naturopathy, Traditional Chinese Medicine, Ayurveda and other traditional practices have long incorporated approaches to improve digestive function as a foundation of overall health. What has changed is that modern research is now catching up, providing a growing body of evidence to support many of these approaches.
What makes naturopathic treatment of IBS in perimenopause different is that it addresses both things at once. Your gut symptoms and your hormonal symptoms are not separate problems requiring separate treatments. They are part of the same picture, and treating them together is not only more efficient, it often produces results that treating them in isolation never achieves.
A naturopathic approach will begin with a detailed case history covering your symptom timeline, diet, lifestyle, personal and family medical history, medications, stress levels, sleep, and anything else that may be relevant to your particular situation. This is the detective work that often reveals connections no single test or specialist has been able to identify.
Treatment may include some or all of the following, depending on what is driving your symptoms:
Restoring hormonal balance and reducing perimenopausal symptoms that are contributing to gut dysfunction, including cortisol dysregulation, sleep disruption and histamine reactivity.
Identifying and addressing food intolerances, using careful elimination and reintroduction rather than permanent blanket restriction, always with nutritional adequacy in mind.
Identifying and addressing nutritional deficiencies which may have occurred through dietary deficiencies (including from long-term restricitive diets such as FODMAP, Paleo, Keto & others) or from damage to the gut itself, preventing proper absorption.
Supporting and restoring microbiome diversity and abundance through diet, specific probiotic strains, and prebiotic fibre, personalised to your situation rather than generic off-the-shelf products.
Improving hydrochloric acid production and digestive enzyme function, which are commonly low in perimenopause and contribute to poor protein digestion, nutrient deficiencies, and vulnerability to gut pathogens.
Repairing intestinal hyperpermeability (leaky gut) where it is present, which is frequently a driver of food allergies, skin conditions, fatigue and systemic inflammation.
Addressing the migrating motor complex and gut motility, particularly relevant if SIBO is a contributing factor.
Supporting the nervous system and stress resilience, because the gut-brain axis means that what affects one always affects the other.
**Private health insurance rebates for naturopathy have been reinstated from 1st April 2026, which means your consultations may now be partially covered, depending on your insurer. Find out what this means for you.
Book a free discovery call here
I have been through this myself. For 25 years I experienced the full range of these symptoms and went from practitioner to practitioner without getting answers. That personal experience, combined with my degree in naturopathy and my Masters’ study in Advanced Naturopathic Medicine (with a specialisation in Human Microbiome and Health), means I bring both clinical knowledge and lived understanding to every consultation.
Most importantly, my patients get results. Not always immediately, because complex conditions that have developed over years do not resolve overnight. But with a personalised, evidence-informed approach that treats the whole person rather than just the symptoms, lasting improvement is entirely possible.
If any of this resonates, I would love to have a conversation with you. Book a free 15-minute discovery call and tell me a little about what is going on for you. There is no obligation, and if I am not the right person to help you, I will tell you honestly.
Frequently asked questions -
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Yes, menopause can contribute to alterations to bowel habits. This can be due to changes in hormone levels which influence histamine producing species in the microbiome, or by altering the pH of the gut which can disrupt the microbiome. Perimenopause is the time when most symptoms are experienced and during this time, an increase in anxiety, anger, and stress generally can then affect the gut.
Also, it’s good to remember that two things can be happening at the same time - it could be menopause AND something else going on, and this is why it’s a good idea to seek the help of an experienced practitioner.
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It does depend on the cause of the diarrhoea, and whether or not it is related to menopause, perimenopause or something else. If it is related to hormone fluctuations or withdrawal, then reducing foods that are high in histamine might help. These are foods/drinks that are fermented, like wine, beer, spirits, kombucha, kim chi, sauerkraut, pickles, vinegar, or condiments that contain vinegar, fish caught more than 1 day ago, meats that are not super fresh.
Caution: Any dietary restriction should be short term to avoid important nutrient deficiencies, unless an allergy or intolerance is identified by your health professional.
Natural strategies for reducing diarrhoea can include:
Specific bulking fibre supplements like slippery elm powder
Specific strains of probiotics, such as Lactobacillus rhamnosus GG, or Saccharomyces boulardii cerevasiae - particularly during or after antibiotic use.
Astringent herbs, as tinctures - such as Rhuem palmatum - Turkey Rhubarb (low dose only), Barberry, Blackberry or Cransbill.
Or, as tea -
Raspberry leaf,
Matcha green tea
Chamomile
Marshmallow root
Chronic diarrhoea should always be investigated for its underlying cause. If symptoms persist, have it investigated by your doctor or naturopath.
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Estrogen can have high surges in perimenopause, and combined with the decline of progesterone can contribute to symptoms of IBS in a number of ways. It may be that there is a sudden onset of IBS symptoms from 40 onwards, in perimenopause and/or menopause, or existing symptoms can become worse.
Also, it’s possible to have IBS due to other factors, during perimenopause or menopause and symptoms can increase during this stage of life. It may be food intolerances, stress, environmental chemical exposures like pesticides or herbicides (like Roundup) which can cause disruption to the microbiome.
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Diarrhoea and constipation are both common changes to digestive function, in menopause and perimenopause. There are a number of factors that can contribute individually or combined to cause this.
Explosive diarrhoea can be uncomfortable, and embarrassing and a sign of something more serious, and can cause digestive damage if it continues. It can occur when there are food intolerances or allergies, due to stress, altered hormone levels of oestrogen and progesterone and following a course of antibiotics or as a symptom of another condition and should always be investigated to identify the root cause.
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Yes! Whilst naturopaths are specialists, we do have areas of interest that we work with a lot. Julie Forrester is a self-confessed microbiome nerd currently completing her masters in Advanced Naturopathic Medicine in Human microbiome and health stream. She’s also a woman who has had her own experience of IBS and menopause, and understands how both of these things can converge to make life uncomfortable, confusing and embarrassing. She works with people of all ages and stages with digestive issues and with perimenopausal and menopausal women.
Working online via Telehealth, she is always ‘near you’ - just a click away, as long as you have a device and the internet and the desire to feel normal again!
Book for a free discovery call here today, and find out if she is the right person to help you.
