Chronic stress is one of the dominant factors in the development of most modern-day diseases. It induces chronically elevated cortisol levels, disrupting various bodily systems, from metabolic and endocrine function to immune and gastrointestinal health.
This article explains the link between cortisol and gut health and provides recommendations for improving both health parameters.

Does Cortisol Affect Your Gut?
Cortisol is a hormone that regulates various bodily functions, such as metabolism, immunity, and inflammatory response. However, it is typically associated with the stress response. When environmental, physical, and psychological stressors challenge our defense and adaptive mechanisms, the hypothalamic-pituitary-adrenal (HPA) axis increases cortisol production in an effort to protect the body. A state of continually elevated cortisol can trigger other hormonal imbalances and wreak havoc on our health, including the digestive system.
How Does Cortisol Affect Gut Health?
Chronically elevated cortisol can damage gut health in several ways.
Gut Inflammation
Stress stimulates the production of pro-inflammatory cytokines and can cause inflammation of the digestive tract. Gut inflammation hinders all gastrointestinal functions, including digestion, nutrient absorption, gut motility, and waste excretion.
Increased Intestinal Permeability (Leaky Gut)
Studies have shown that stressful situations and increased cortisol can damage the intestinal epithelial barrier, increasing intestinal permeability and allowing pathogens to enter the bloodstream. This condition is also known as leaky gut and it is followed by uncomfortable gastrointestinal symptoms, including bloating, gas, cramping, abdominal pain, diarrhea, and constipation.
Gastrointestinal Conditions
Inflammation of the GI tract and leaky gut allow toxins, pathogenic bacteria, and undigested food to enter the bloodstream, potentially causing or exacerbating chronic digestive conditions. They include irritable bowel syndrome, Crohn’s disease, ulcerative colitis, small intestinal bacterial overgrowth (SIBO), nutrient malabsorption, and more.
Gut Microbiota Dysbiosis
The large intestine is home to millions of microorganisms (bacteria, viruses, fungi, etc.), which play a key role in digestion, metabolism, immunity, and central nervous system activity. Elevated cortisol and its damaging effects on gut health can cause a reduction in the number of beneficial bacteria, such as Lactobacillus and Bifidobacterium, and overgrowth of pathogenic microorganisms.
A disbalance in optimal microbiota levels and composition is called gut dysbiosis. Common symptoms include bloating, gas, abdominal discomfort, and irregular bowel movements. Untreated dysbiosis can lead to fatty liver disease, metabolic syndrome, food intolerance, malnutrition, and other more severe conditions.
Abdominal Weight Gain
High cortisol levels increase blood sugar and inhibit insulin production. This leads to increased appetite, sugar cravings, slower metabolism, and disrupted sleep, which can result in weight gain over time. Hormonal weight gain is characterized by fat accumulation in the abdominal region.
How to Diagnose Poor Gut Health Due to Cortisol?
There are several ways to assess whether a patient’s gut problems are associated with high cortisol and chronic stress.
- Cortisol testing (blood or saliva) – Measuring cortisol levels throughout the day helps doctors establish the stress hormone’s pattern and whether the patient’s digestive disorders are related to stress.
- Comprehensive stool analysis – Stool tests show the patient’s microbiome status and the ratio of beneficial and pathogenic microorganisms in the GI tract. It can also detect other related markers like calprotectin, an indicator of inflammation, and zonulin, associated with a leaky gut. These markers can reveal gut disorders potentially caused by stress.
- Breath test – This diagnostic examination can help detect SIBO, which impairs digestion and nutrient absorption. Chronic stress may contribute to bacterial overgrowth.
How to Fix Cortisol Levels and Improve Gut Health?

Patients can significantly improve their hormonal status and gut health by managing stress and adopting a healthier diet. Doctors recommend the following natural strategies to lower cortisol and restore a healthy gut microbiome.
Balanced Diet
A diet is one of the most critical and direct factors in gut microbiota composition and function. Unhealthy habits, such as eating a lot of sugary and processed foods, can cause cortisol spikes, destroy beneficial bacteria, and allow pathogenic microbes to thrive.
Medical experts recommend anti-inflammatory diets, such as the Mediterranean diet, as the best solution for stress-induced inflammation and digestive concerns. These diets are based on the following foods:
- Fiber-rich fruits and vegetables
- Legumes
- Whole grains
- Fish, nuts, and seeds (rich in omega-3 fatty acids)
- Fermented foods, such as sauerkraut, pickles, and yogurt (rich in probiotics)
- Herbs and spices (high in antioxidants)
Anti-inflammatory meal plans provide numerous health benefits and lower the risk of cardiovascular, neurological, gastrointestinal, and other chronic diseases.
Supplements for Stress
Supplements for stress containing adaptogenic (stress-relieving) botanicals and antioxidant vitamins and minerals can greatly contribute to stress management, if combined with other healthy lifestyle habits like a balanced diet. Well-researched ingredients known for their stress-relieving and gut-supporting effects include Ashwagandha, Rhodiola rosea, chamomile, vitamins C, B, and D, magnesium, and more.
Probiotics and Prebiotics
Probiotics and prebiotics are emerging as a powerful aid in restoring a healthy microflora and lowering inflammation. Probiotics are live microorganisms that increase the number of beneficial bacteria in our digestive tract, and prebiotics feed probiotics.
Some of the most extensively studied probiotics include Lactobacillus acidophilus, Lactobacillus plantarum, Bifidobacterium longum lysate, Saccharomyces boulardii, etc. They are present in fermented foods and probiotic supplements. Prebiotics are abundant in fruits and vegetables, including garlic, onions, bananas, oats, legumes, mushrooms, and more. Consuming probiotic and prebiotic foods and supplements can support the patient’s efforts to regulate cortisol response and promote a diverse microbiome.
Note: Learn about the differences between prebiotics, probiotics, and postbiotics and the best way to use them for digestive, mental, and skin health.
Improved Sleep
Melatonin and cortisol have a bidirectional relationship. When one is out of balance, it negatively impacts the other hormone’s levels. Disrupted sleep can also affect one’s dietary choices and contribute to gastrointestinal problems.
Prioritize a healthier sleeping routine, going to bed early and waking up at the same time. Aim for seven to nine hours of uninterrupted sleep every night. Use supplements for sleep and practice stress-relieving techniques, such as breath work and meditation, to achieve your goals.
Regular Exercise
Numerous studies provide evidence of the beneficial impact of regular exercise on our physical, mental, and emotional health. Moderate-intensity activities promote the production of feel-good hormones, helping to lower stress and balance cortisol levels. Exercise also increases the microbiome’s diversity and supports beneficial gut flora, strengthening the intestinal barrier and regulating gut motility.
Stress Management
Besides regular exercise, a nutritious diet, and other essential habits, patients can employ the following strategies to reduce stress and improve gut health.
- Meditation
- Deep breathing exercises
- Yoga
- Nature walks
- Keeping a pet
- Social activities
- Relaxing music
- Fun hobbies
How Long Does It Take to Heal Poor Gut Health Due to Cortisol?
It takes time to restore a hormonal homeostasis and heal digestive issues. Patients with mild symptoms feel an improvement within days or weeks of adopting healthier lifestyle habits. However, those with more severe problems need to be persistent and patient to experience significant symptom relief, which may take months.
Patients with chronic digestive disorders like irritable bowel syndrome and inflammatory bowel disease typically need medical supervision. Some may require medication and medical treatments in combination with lifestyle modifications and supplements.
Does Poor Gut Health Affect Cortisol Levels?
Poor gut health can exacerbate inflammation and stress and contribute to chronically elevated cortisol levels. An imbalanced gut microbiome may interfere with the gut-brain axis, disrupting communication between the digestive and nervous systems. This can contribute to a cascade of issues, including hormonal imbalances, impaired neurotransmitter production (such as serotonin and GABA), heightened immune responses, and the release of pro-inflammatory agents.
Conclusion
High stress and cortisol levels can seriously impact our digestive health and lead to severe medical conditions. Restoring microbial balance through targeted nutrition, probiotics, and digestive support is essential for calming the nervous system, regulating cortisol, and supporting overall emotional and physical resilience.


