How Chronic Stress can Wreck Your Digestion
Melissa McDonald B.Sc., Clinical Naturopath
Stress is often referred to as the “silent killer” due to its effects on our body without us actually realising it. One area in particular is your gut health, due to the hormone cortisol. This guy can disrupt your ability to make hydrochloric acid, reduce your absorption of nutrients which leads to deficiencies and long-term digestive issues.
In this blog, we’ll explore how cortisol works, its effect on digestion, and how stress can upset the delicate balance of your gut microbiome. Plus, I’ll share practical tips to help you restore your cortisol and support your gut health naturally.
How Cortisol Works
Contrary to popular belief, we actually NEED cortisol in our body. It gets you up and out of bed in the morning, it’s released to regulate blood sugar levels, influence memory and has an anti-inflammatory effect on our body (to name a few).
This all comes from the adrenal glands, which release cortisol in response to stressful situations, known as the “fight or flight” response.
In my opinion, the most concerning part about cortisol is when we produce too much, too many times throughout the day or the week, which can often go on for months at a time.
Your adrenal glands reach a point where they become tired from all that hard work regulating all of the stressful events in your life. However, your brain and your body doesn’t discriminate stressful events – whether that’s reading a horrible email at work, someone passing away or getting sick, or over-exercising and under eating. Physiologically the cortisol produced from these experiences is just as damaging as each other.

The Impact of High Cortisol on Digestion
When cortisol levels are consistently high due to stress, the digestive system is often one of the first areas to suffer. Here’s how:
High cortisol signals your body to divert energy away from digestion to focus on survival. The vagus nerve stops sending signals to your parietal cells, reducing hydrochloic acid and pepsin which are key to breaking down your food. Then, the undigested food moves more slowly through your digestive tract, leading to bloating, constipation, and reflux issues.
Chronic cortisol exposure can increase the permeability of the gut lining, often referred to as “leaky gut.” This allows toxins, partially digested food, and bacteria to leak into the bloodstream, causing inflammation and contributing to various health problems.
Stress can interfere with the gut’s ability to absorb key nutrients. This leads to malnutrition, even if you’re eating a healthy diet. Over time, this can cause fatigue, weakened immunity, and other health concerns.
Gut imbalances Caused by Stress
Your gut is home to trillions of microorganisms—bacteria, viruses, fungi—collectively known as the gut microbiomen (there are some microbes in your gut than cells in the human body!). These microbes are essential for digestion, immune function, and overall health. However, stress and elevated cortisol can upset the balance of this diverse ecosystem, leading to gut dysbiosis (an imbalance of good vs. bad bacteria).
Chronic stress reduces your good gut bugs, which creates an enivornment for the bad gut bugs to thrive. This can lead to conditions like irritable bowel syndome (IBS), small intestinal bacterial overgrowth (SIBO), small intestinal fungal overgrowth (SIFO), large intestinal bacterial overgrowth (LIBO) or large intestinal fungal overgrowth (LIFO). These conditions are often ruled out in many of my patients (especially with IBS), with blood work; comprehensive functional stool testing & breath testing.
Practical Steps to Restore Gut Health
The good news – you CAN take steps to counteract the negative effects of stress on your gut.
Here are some practical strategies to restore balance and improve digestive health:
- 1
Identify your stressors and find ways to remove them for your life or manage them more efficiently. For example, boundary setting has helped significantly within my work and home life. I worked closely with a psychologist for a few months to help with this process.
- 2
Incorporating stress-reducing practices like meditation, yoga, or deep breathing exercises that are known to lower cortisol levels and support overall gut health.
- 3
Eat more fibre rich foods and try to incorporate a different vegetable into your diet
- 4
Fermented foods (like sauerkraut, kefir, and kimchi), and prebiotics (like garlic, onions, and leeks) to support a healthy gut microbiome, but don’t over-do it.
- 5
Lack of sleep increases cortisol levels, so aim for 7-9 hours of quality sleep each night to help reduce stress and restore gut health.
- 6
Physical activity can lower cortisol levels and improve gut motility, reducing issues like bloating and constipation.
- 7
Certain herbs like ashwagandha, rhodiola, and licorice root have been shown to help balance cortisol levels. Additionally, herbal medicines like chamomile and peppermint can soothe digestive discomfort.
- 8
Probiotic supplements can help replenish good bacteria in your gut, while digestive enzymes and other supplements may support better nutrient absorption. I always recommend doing stool testing before utilising probiotics, as they may not necessarily help you, or may make things worse.
The cortisol-gut connection is a clear reminder of how deeply stress can affect our bodies, especially digestion.
If you’re experiencing persistent digestive issues related to stress, book a Naturopathy consultation with our Clinical Naturopath Melissa McDonald today to develop a personalised plan to manage your stress and support your gut health naturally.
Naturopathic medicine offers a holistic approach to managing chronic gut issues and symptoms, addressing the root causes while supporting the body’s natural healing processes.
With a focus on personalized care and natural remedies, Naturopathy can be a valuable complement to conventional treatments.
If you’re struggling with lingering symptoms of gut issues and seeking effective relief, consider booking an appointment with our experienced Naturopath, Melissa McDonald.
Together, we can tailor a treatment plan to support your recovery and optimize your overall well-being. Don’t hesitate to take the first step towards feeling better today.
Melissa McDonald B.Sc., Clinical Naturopath
References
Brady, C., Denora, M., Shannon, I., Clark, K. J., & Rich, A. (2017). Intestinal Transit Time and Cortisol-Mediated Stress in Zebrafish. Zebrafish, 14(5), 404–410. https://doi.org/10.1089/zeb.2017.1440
Foster, J. A., Rinaman, L., & Cryan, J. F. (2017). Stress & the gut-brain axis: Regulation by the microbiome. Neurobiology of stress, 7, 124–136. https://doi.org/10.1016/j.ynstr.2017.03.001
Madison, A., & Kiecolt-Glaser, J. K. (2019). Stress, depression, diet, and the gut microbiota: human-bacteria interactions at the core of psychoneuroimmunology and nutrition. Current opinion in behavioral sciences, 28, 105–110. https://doi.org/10.1016/j.cobeha.2019.01.011
Disclaimer: Before taking any herbal medicines or nutraceuticals, it is essential to check for potential interactions with any pharmaceutical medications you are currently using. For any other questions or concerns, please consult your naturopath, doctor, or health practitioner.







