Why A Healthy Diet Migh Not Be Enough For Gut Issues, Autoimmune Conditions And Chronic Fatigue

I used to believe that eating healthy and removing “trigger foods” from my diet was the main answer to all my health troubles. I diligently tried elimination diets and followed every piece of nutritional advice I could find. Yet, despite these efforts, after many years, I still struggled with chronic fatigue in the morning, bouts of muscle weakness, and an unpredictable immune system that seemed to overreact at the smallest thing. To my surprise, I discovered that it wasn’t just about what I ate—my stress response and emotional health played an even more significant role.

Beyond Nutrition: A Look at Stress and Emotional Regulation

From personal experience, I learned that health problems often start in our brains—particularly in how we perceive, process, and respond to chronic stress. It turns out our brains cannot differentiate between actual stress, something we merely imagine, or an anticipated stressful scenario we play in our head. Each scenario triggers the same stress response, initially leading to elevated cortisol levels. Over time, this can devolve into a constant state of high cortisol, or—for some people—a gradual drop that leaves them with a blunted or “flatlined” cortisol pattern.

When I started paying closer attention to how I handled stress—my emotional swings and coping mechanisms—I realized I was constantly in fight-or-flight mode. The more I dug into the science, the more I understood that my Hypothalamic-Pituitary-Adrenal (HPA) axis was likely struggling and there was a constant activation of my sympathetic nervous system. Under normal circumstances, stress triggers the release of cortisol to help us cope. But when stress becomes chronic, these signals can overload the system, leading to HPA axis dysregulation—where either too much or too little cortisol circulates, and the body isn’t adapting the way it should. As a result, relatively minor physical or psychological stressors may be converted into an inflammatory response.

Symptoms: Low Cortisol in the Midst of High Stress

Even though I was experiencing relentless stress, I started noticing symptoms that actually suggest low cortisol or a desensitized HPA axis:

• Gastrointestinal issues: My gut would act up seemingly at random, even though I was eating whole foods, organically grown, low glucose and no processed foods. I later realized this was linked to cortisol’s role in regulating inflammation and the immune response in the GI tract.
• Dysfunctional immune system: I’d catch colds easily from my school-aged daughter—which worsened my chronic sinus issues—yet I also felt constantly “inflamed.” Because cortisol plays a balancing role in immunity, if it’s out of balance, you can become more susceptible to infections and chronic inflammation.
• Muscle weakness and fatigue: I found daily tasks surprisingly exhausting, which often happens when the body lacks proper cortisol rhythms to support energy metabolism.
• Exercise intolerance: Despite my best efforts, working out felt like an uphill battle—another sign that my cells weren’t getting the energetic support they needed.
• Low Blood Pressure: Sometimes I felt lightheaded or dizzy, especially when standing up quickly. Normally, cortisol helps maintain vascular tone and fluid balance, so insufficient or dysregulated cortisol production can lead to lower blood pressure and these dizzy spells.
• Memory problems: Brain fog and trouble recalling details can tie back to dysregulated cortisol, as the hormone is involved in cognition and mental clarity.
• Mood Changes: Anxiety, depression, or irritability.

As I researched further, I discovered that this mismatch—high perceived stress but low cortisol output—can happen when the adrenals and their mitochondria (the energy powerhouses in our cells) become overwhelmed, eventually leading the brain to dial down the stress response. This maladaptation can be compounded by genetic predispositions, nutrient deficiencies, and other factors.

Connecting Mitochondrial Function

One critical piece I learned is that cortisol production itself depends on a healthy mitochondrial function in the adrenal cortex. When we’re under constant stress, these mitochondria produce larger amounts of cortisol, generating oxidative byproducts in the process. Over time, if there’s not enough nutritional support (like vitamins C and B, magnesium, and antioxidants), these mitochondria get strained.

Basically any mitochondrial dysfunction—due to oxidative stress, impaired ATP production, genetic variants in mitochondrial enzymes, or chronic inflammation—can reduce its efficiency, limiting cortisol production – contributing to low energy, brain fog, and inflammatory flare-ups.

Mitochondrial Health Affects Overall Energy

If mitochondria are underperforming, cells struggle to produce ATP (the body’s main energy molecule). Low ATP availability affects all energy-demanding processes, including:

• Maintaining normal adrenal function.
• Supporting the hypothalamic-pituitary-adrenal (HPA) axis signaling.
• Meeting the metabolic demands of cells throughout the body.

Thus, mitochondrial dysfunction can both directly reduce cortisol synthesis and indirectly worsen symptoms of low cortisol by limiting energy production.

Overall How Chronic Stress Can Ultimately Lead To Reduced Cortisol Output

1. Early Stage: High Stress → High Cortisol

• Initial Response: When stress first becomes chronic, the HPA axis (Hypothalamus–Pituitary–Adrenal axis) is typically in overdrive, leading to consistently elevated cortisol.
• Adaptive Goal: This high cortisol output helps the body cope with continued stress (increasing blood glucose, suppressing excessive inflammation, etc.).

2. Transition to Dysfunction: The “Wearing Down” Phase

a) Feedback Loops and Receptor Changes

• Receptor Downregulation: Overexposure leads to less sensitive receptors in the hypothalamus/pituitary and structural changes in stress-related brain areas.

b) Mitochondrial Strain in Adrenal Cells

• Cortisol Synthesis: Relies on healthy mitochondria. Under chronic demand, these cells produce excess ROS (reactive oxygen species).
• Damage Over Time: Prolonged oxidative stress and nutrient depletion impair mitochondrial function, reducing cortisol output.

c) Inflammatory/Immune Factors

• Cytokine Disruption: Chronic stress elevates pro-inflammatory signals that can either amplify or blunt cortisol production, depending on the stage and location of inflammation.

3. Late Stage: Reduced Cortisol Output

When stress stays high for a long time, we often see HPA axis dysregulation or a “flattened” cortisol curve:

1. Blunted Morning Peak: Instead of the normal morning surge, some people have low cortisol in the morning (leading to fatigue and difficulty getting going).
2. Reduced Flexibility: The HPA axis becomes less responsive to daily demands or acute stressors.
3. “Adrenal Fatigue” vs. HPA Axis Dysregulation: While “adrenal fatigue” is a popular but somewhat controversial term, the more precise physiological description is HPA axis dysregulation—where the signaling and feedback loops are out of sync, and mitochondrial inefficiency in the adrenal glands can be part of the problem.

Summing Up

• High Cortisol Initially: Chronic stress does push cortisol levels up for a while.
• Over Time, System Dysregulation: Because of sustained high levels, negative feedback on the hypothalamus and pituitary plus potential mitochondrial strain in adrenal cells can lower cortisol output when it is actually needed.
• It’s Not Always a Simple On/Off: Some people with chronic stress will still have high cortisol, others low, and some have a flattened (upside-down) rhythm—it depends on how each person’s HPA axis and cellular machinery adapt over time.

Embracing a Holistic Approach

Ultimately, focusing on restoring mitochondrial resilience, reducing chronic inflammation, and rebalancing the HPA axis (via both lifestyle and targeted therapies) can help the body regain the ability to produce and effectively use cortisol.

My journey, and studying at the Institute For Integrative Nutrition, taught me that true healing requires addressing every dimension:

• Emotional regulation and stress management: Tools like mindfulness (being aware of your thoughts, emotions when their arise), breathing exercises to calm the stress response, addressing underlying emotional traumas or chronic anxiety/depression, EFT “Tapping”, somatic practices, journaling or any other activities that encourage grounding, joy and calmness.
• Nutrient-Dense, Anti-Inflammatory Diet: Yes, food still matters—a colored whole food approach, ensuring adequate clean protein, healthy fats, complex carbs, and key vitamins and minerals. Excess Refined Sugar and highly processed foods can spike inflammation and dysregulate blood glucose (which can stress the adrenals). Key Nutrients for Adrenal and Mitochondrial Support: Vitamin C: The adrenal glands have a high concentration of vitamin C; it’s needed for cortisol synthesis. Also B Vitamins (especially B5, B6, B12, Folate) which are critical for energy production and HPA axis function. Magnesium: involved in stress regulation and mitochondrial function. And omega-3 fatty acids: anti-inflammatory effect that can help modulate autoimmune activity.
• Gut Microbiome Health: Up to 70% of the immune system is in the gut. Supporting healthy microbiome balance (via probiotics, fermented foods, prebiotic fibers) may reduce systemic inflammation and autoimmune flare-ups. Gut microbiota can influence the HPA axis function through the activity of cytokines, prostaglandins, or bacterial antigens.
• Quality sleep and circadian rhythm: A consistent sleep-wake cycle of 7-9 hours. Getting sunlight soon after waking supports cortisol’s natural morning peak and aligns the circadian rhythm. and also dim lights and reduce stimulation at night to encourage melatonin release and cortisol lowering. This will help with resetting cortisol patterns and supporting mitochondrial repair.
• Targeted supplementation: For some, adaptogens (like ashwagandha or rhodiola rosea), anti-inflammatories (like curcumin, omega-3 fatty acids), or mitochondrial support (CoQ10, magnesium) can be game-changing. But these are best introduced after cleaning up your diet and eating patterns.
• Balanced Movement and Exercise: engaging in regular, moderate-intensity activities (e.g., brisk walking, swimming, light jogging, trampoline jumping) supports mitochondrial health and helps regulate cortisol.
• Environmental Toxin Reduction: toxins and hormone disruptors: pesticides, plastics (BPA, phthalates), and heavy metals can burden the body and disrupt endocrine function.
• Lifestyle Adjustments: Use natural cleaning products, filter drinking water, choose organic produce when possible to reduce pesticide and herbicide expose, store food in glass/stainless steel containers. Reducing toxin load supports overall metabolic and immune health.
• Community and relationships: Healthy social connections and a good support system can buffer the impact of stress. Positive relationships correlate with lower chronic stress markers and better immune regulation. Healthy boundaries: saying “no” when overwhelmed, structuring downtime, and avoiding continuous work/stress cycles.

By integrating these elements, I’ve seen improvements in my energy levels, immune health, and overall well-being. The key takeaway? Health is a dynamic puzzle—the solution doesn’t lie in one single action (like eliminating gluten or dairy) but in carefully supporting the body’s stress response, emotional balance, immune function, and nutrient needs.

Best is to start with incorporating emotional regulation and stress management methods into your daily routine, so you give your body and mind a chance to recover from chronic stress, protect (or restore) mitochondrial function, and maintain a healthier HPA axis response. And then you can adress the other needs one by one.

Now, I view every stressful situation, dietary tweak, or lifestyle choice as a piece of my broader health picture. I’ve come to appreciate that my brain, body, and environment all intersect to form my unique stress response—and my health outcomes follow suit. Recognizing this bigger picture was empowering—it helped me see that by adjusting the ways I think, feel, move, and eat, I can gradually shift my HPA axis toward resilience and reclaim my vitality.

Disclaimer: The content in this blog is for informational purposes only and should not replace professional medical advice. If you’re experiencing chronic symptoms, consider consulting a qualified healthcare professional.