Root Causes of Chronic Pain & Treatment Solutions

by | Mar 24, 2022 | Chronic Illness, Digestive Health, Hormone Health, Naturopathy, Nutrition

Whether your pain is widespread, arthritis, headaches or muscle pain, there is a root cause.

Inflammation is typically the main cause of chronic pain – when the brain perceives inflammation or injury via the nervous system, pain is perceived.

In those with chronic pain, the brain becomes wired to perceive pain

Conventional medicine aims to manage the pain by prescribing anti-inflammatory and analgesic medications, but we need to ask, where is the inflammation coming from?


Causes of Chronic Pain

Nutrient deficiencies

When your body is lacking the nutrients it needs to function, inflammation and pain can result, especially if it includes nutrients needed to produce neurotransmitters such as serotonin, or sex hormones such as progesterone.

Common deficiencies include:

Vitamin D: since vitamin D is immune modulating, deficiencies can cause immune problems and inflammation.

Omega 3: not getting enough healthy fats prevents your cells from functioning optimally, which can contribute to chronic pain.

Vitamin B12: deficiency can lead to neuropathy and other pain conditions. Needed to produce several neurotransmitters including serotonin, which modulates pain perception and sensitivity.

Dr. Kristin Spark, ND and Dr. Stacy Burke, ND both offer nutrient testing via blood tests.

Mitochondria dysfunction

Your mitochondria are the powerhouses of your cells: they make energy (ATP) for your body. Inflammation can cause mitochondrial dysfunction, which can perpetuate fatigue and pain.

Often this inflammation comes from inflammatory gut bacteria, yeast overgrowth, stress and a poor diet.

Dysbiosis (gut microbiome imbalance)

Chronic gut dysbiosis creates inflammation not just in your gut, but throughout your body, including your brain. They do this by releasing toxins, triggering the immune system to release inflammatory cytokines and causing leaky gut and food reactions. 

Poor diet

The standard American diet is high in processed foods, sugar, and red meats, and is low in fruits and vegetables, which causes inflammation by depriving your body of the nutrients it needs to function.

It also promotes imbalanced blood sugar, which further perpetuates inflammation.

Chronic stress

Stress triggers the immune system to release inflammatory molecules called cytokines which can trigger pain. It also promotes the growth of inflammatory gut bacteria which also triggers inflammation and pain.

Adrenal depletion (aka “burnout”)

Over time, chronic stress takes a toll on the adrenal glands. Eventually they become depleted and are not able to keep up with the demand to produce cortisol. Cortisol is needed to dampen inflammation, so at this point, inflammation goes unchecked and can trigger chronic pain.

Brain chemicals such as serotonin are also needed to modulate pain and can become dysregulated due to stress.


Trauma keeps the nervous system in a stressed, “fight or flight” state. The post-trauma brain can re-wire it’s “circuits” to interpret patterns, people, situations, and stressors as more stressful than others would find.

This triggers the release of stress hormones and causes other hormone imbalances, and wires the nervous system to be on guard for pain, resulting in heightened pain sensitivity.

Lack of sleep

Sleep is when the body restores itself. It allows cells to heal and your lymphatic system to flush out metabolic wastes. Poor quality or insufficient sleep keeps your body in an inflammatory state – stuck in fight or flight stress mode it is hyper-vigilant to threats.

Hormone imbalance

Sex hormones have a powerful effect on the body and directly impact pain. Common sex hormone (estrogen and progesterone) imbalances in menstruating women can lead to increased pain. Additionally, imbalanced thyroid hormones, testosterone, and insulin hormone levels can contribute to inflammation, blood flow changes, blood sugar changes, and ultimately chronic pain. 

Toxin exposure (bath and body products, pollutants, pesticides, herbicides on food)

Toxins must be detoxified by the body via the liver, kidneys, skin or digestive system.

This places a burden on the body and creates cellular inflammation. The body uses up its antioxidant resources, which are needed for optimal cellular function, creating inflammation, pain & fatigue.

Injury, poor posture & repetitive strain:

Jobs or other activities that include repetitive motions can cause pain and reduced mobility in a joint or muscle. Once a muscle or joint is constricted, lack of blood flow and nerve pinching can trigger chronic pain.

Pain management solutions


1. Find the root cause

To find the root cause you will need to work with a practitioner to determine which of these root causes are triggering your chronic pain.

This may include functional testing such as :

– blood work: testing for nutrient deficiencies, imbalanced blood sugar, CRP & ESR (inflammatory markers), sex hormone and thyroid hormone imbalances.

– adrenal testing: testing for adrenal fatigue

– urine testing: DUTCH test for sex hormones and metabolites and/or adrenal hormones.

– stool testing: testing for dysbiosis; a microbial imbalance that can trigger systemic inflammation, as well as indicate potential serious inflammation markers. 

Your practitioner will also recommend a personalized protocol including supplements, dietary changes and lifestyle adjustments.


2. Diet

Your diet has a significant impact on your levels of inflammation and pain.

Processed foods: diets high in processed foods are inflammatory. Due to the nature of these foods, the inflammatory fats, high sugar content, preservatives and other chemicals create inflammation in the digestive tract, which triggers inflammation in the brain, creating pain. Reduce processed foods as much as possible. 

Fibre: get more fruits, vegetables, legumes, nuts, seeds, and whole grains which are high in fibre. Fibre is crucial to feed healthy gut bacteria, which not only manages digestive heath, but keeps inflammation and pain at bay. These foods are also very high in nutrients like vitamins, micro-minerals, fatty acids, and proteins. 

Antioxidants: your cells require antioxidants to function and provide your body with energy.

If you find healthy eating overwhelming, or you struggle with bloating or food sensitivities, book an appointment with one of our naturopathic doctors for support. Check out our 8 tips for mindful eating! 


3. Manual treatment modalities

Massage therapy and chiropractic can be helpful,  especially for those with chronic musculoskeletal pain or injuries.

Massage therapy: reduces pain by:

– improving circulation

– reducing stress and improving sleep

– improving muscle &  joint mobilization

– lymphatic drainage through massage or cupping


– aligns the spine and reduces pain by releasing pinched nerves and allowing the surrounding muscles to function optimally

– reduces headaches & migraines

– relieves and manages chronic back pain, carpal tunnel and more


Our naturopathic doctors Dr. Kristin Spark, ND and Dr. Stacy Burke offer Traditional Chinese Medicine acupuncture that involves the insertion of fine needles in specific locations of the body.

Acupuncture provides pain relief by stimulating the body’s natural healing processes, increasing blood flow, and reducing stress. It also shifts the nervous system into a relaxed state where healing occurs.

It releases endorphins and fascial stimulation works on the immune system to restore balance and optimal functioning.

 Stress Management

Stress itself triggers pain and can program the body and brain to be wired for chronic pain.

Even those who eat well, take supplements and exercise may still experience pain if they are not managing their stress levels.

Some practices to add to your daily routine:

– deep breathing, meditation, time in nature, spending more time doing what you enjoy with those you love. 


Chronic pain is a complex condition to manage, and an integrative approach may offer improved outcomes. Seeking support from a variety of practitioners addresses the many causes of pain. You can live a better life, while managing pain conditions!  

Statements, treatments, and advice are not to be interpreted as medical advice. Always seek the advice of a licensed qualified practitioner before starting any new treatments, vitamins, or supplements. 


Verdure Wellness Clinic in Waterloo, ON offers naturopathic medicine, acupuncture, nutrition consulting, massage therapy and chiropractic care. Our team of health practitioners offer a variety of services with your best health and wellness in mind.

305-55 Erb Street E, Waterloo, Ontario   •    519.742.0691

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