Thank you! Your submission has been received!
Oops! Something went wrong while submitting the form.
Subscribe to the Magazine for free
Subscribe for free to keep reading! If you are already subscribed, enter your email address to log back in.
Thanks for subscribing!
Oops! Something went wrong while submitting the form.
Are you a healthcare practitioner?
Thanks for subscribing!
Oops! Something went wrong while submitting the form.

A Functional Medicine Eczema Protocol: Testing, Nutrition, and Supplements

Medically reviewed by 
A Functional Medicine Eczema Protocol: Testing, Nutrition, and Supplements

Eczema, a chronic skin condition affecting over 30 million Americans, continues to present a challenge for patients and healthcare providers. The prevalence of eczema has surged over the years, with a staggering 15-30% of children and 2-10% of adults affected globally (17). Symptom-based, traditional treatments often only provide temporary relief, leaving individuals wanting a lasting solution. However, by addressing the causative factors underlying symptom presentation, a functional medicine and holistic approach to eczema provides hope for longer-lasting symptom resolution and improved quality of life.


What Is Eczema?

Eczema refers to a group of inflammatory skin conditions characterized by red, itchy, and inflamed patches on the skin. It is a non-contagious condition that often begins in childhood but can persist into adulthood. (3, 10

There are seven subtypes of eczema: atopic dermatitis, contact dermatitis, dyshidrotic eczema, neurodermatitis, nummular eczema, and seborrheic dermatitis. While each type of eczema has unique triggers, it is possible to have multiple types of eczema simultaneously. Atopic dermatitis is the most common type of eczema that occurs in patients with a personal or family history of allergic conditions. (3)

Symptoms of Eczema

Eczema can vary in severity, from mild dryness and occasional itching to intense itching, pain, and thickened skin. The affected areas of skin will appear flaky and bumpy, often with excoriations (scratches). Rashes can be red, pink, purple, brown, or gray, depending on skin tone. (3

Eczematous rashes can occur anywhere on the body, but the rash distribution often varies depending on the patient's age. Infants tend to have involvement of their face, especially the cheeks, forehead, and around the mouth. As the child ages, the rash tends to become more localized to the extensor surfaces of the wrists, elbows, ankles, and knees. In contrast, adults are often affected with rashes located on the flexural surfaces of the elbows and knees. (6, 17)

Besides the classic rash, other physical exam findings are often noted in patients with eczema. Crease-like wrinkles just below the lower eyelid (Dennie-Morgan lines) and a transverse crease across the bridge of the nose ("allergic salute") are common in those with eczema and concurrent allergies. People with eczema may also have hypopigmented patches or fine-scaling plaques on the face. (17

Eczema can significantly impact a person's quality of life, causing an increased risk of skin infection, sleep disturbances, and emotional distress. (14

What Causes Eczema?

Eczema results from a combination of genetic and environmental factors that stimulate the immune system and disrupt the skin barrier. 

Research shows there is a genetic component to eczema, supported by the fact that eczema is more common in individuals with a family history of eczema, dermatitis, asthma, and allergies (3). 50-70% of patients with eczema have a genetic mutation in the filaggrin (FLG) gene, which is responsible for forming the outermost protective layer of skin. Defects in the FLG gene result in a dysfunctional skin barrier, leading to an impaired ability to retain water, modulate the skin barrier's pH, and fight off infectious pathogens. (6, 10)

People with eczema have reduced numbers of beta-defensins in the skin, which protect the skin against infectious agents  (17). A decrease in these proteins leads to increased colonization and infection with opportunistic pathogens, especially Staphylococcus aureus and Candida albicans

Recent research has highlighted the gut microbiome's significant influence on skin health, bringing rise to the notion of the gut-skin connection. The gut microbiome plays a crucial role in modulating the immune system, regulating inflammation, and maintaining the integrity of the intestinal barrier. When imbalances occur in the gut microbiome, commonly known as dysbiosis, it can lead to increased intestinal permeability, referred to as "leaky gut." This compromised barrier function allows toxins, pathogens, and undigested food particles to enter the bloodstream, triggering an immune response and systemic inflammation. This inflammation can manifest on the skin as various dermatological conditions, including eczema. Moreover, the gut-skin connection extends beyond inflammation, as the gut microbiome produces metabolites that can directly impact the skin's health and appearance. (6)

Allergies play a significant role in the development and exacerbation of eczema. Individuals with eczema tend to be predisposed to allergic conditions such as asthma, hay fever, and food allergies. The immune system in people with eczema reacts abnormally to certain substances, known as allergens, triggering an inflammatory response in the skin. Common allergens that can exacerbate eczema symptoms include dust mites, pet dander, pollen, mold, certain foods (such as dairy, eggs, nuts, and shellfish), and irritants like harsh soaps or detergents. When exposed to these allergens, the immune system releases histamines and other inflammatory mediators, leading to itching, redness, swelling, and the characteristic rash associated with eczema. Additionally, allergies and eczema can create a vicious cycle, as eczema flare-ups can further sensitize the skin, making it more prone to allergic reactions. (10)  

Functional Medicine Labs to Test for the Root Cause of Eczema

Outlined below are common specialty labs ordered by functional medicine providers to individualize a root-cause treatment approach for eczema.

Comprehensive Stool Test

A comprehensive stool test measures biomarkers to evaluate for intestinal dysbiotic patterns, intestinal inflammation, and intestinal permeability that may influence gut and skin barrier function.


A comprehensive IgE panel screens for allergic responses against environmental and dietary allergens.

A statistically significant correlation has been noted between C. albicans IgE antibodies and the severity of atopic dermatitis. Additionally, skin manifestations improve with antifungal therapy. Therefore, C. albicans IgE antibodies should be ordered if not already excluded in other allergy testing. 

Functional Medicine Labs to Test That Can Help Individualize Treatment for Eczema Patients

Additional specialty tests can be considered for patients with eczema to refine treatment protocols.

Micronutrient Testing

Certain nutrients are known to be essential for skin health and reducing inflammation. Nutrient deficiencies may result from impaired gut function, dysbiosis, and dietary restrictions. A micronutrient test can screen for deficient or suboptimal levels of essential nutrients, such as vitamin C and zinc, required to combat inflammation and promote healing within the skin. 

Food Sensitivities 

Children with eczema commonly have delayed (non-allergic) reactions to food sensitivities, most often including dairy, gluten, and eggs (10). Food sensitivity testing can confirm the presence of food sensitivities so that a therapeutic elimination diet can be initiated to reduce immunologic hyperactivity and support intestinal healing.


Conventional Treatment for Eczema

Conventional treatment interventions for eczema typically involve a combination of topical treatments and oral medications. Topical corticosteroids are commonly prescribed to reduce inflammation and itching, while moisturizers help hydrate the skin and maintain its barrier function. In more severe cases, immunosuppressant medications like calcineurin inhibitors may be used. Antihistamines are sometimes prescribed to relieve itching and promote sleep. (2

Functional Medicine Treatment Protocol for Eczema

Conventional treatments primarily focus on symptom management rather than addressing the underlying causes of eczema. This has led to the exploration of alternative approaches that more strongly emphasize therapeutic diets, dietary supplements, and other complementary interventions to correct the underlying causes of eczema, reduce inflammation, and restore the skin barrier's integrity. 

Therapeutic Diet and Nutrition Considerations for Eczema

A therapeutic elimination diet that removes identified IgE and IgG-mediated food triggers should be a primary goal of managing patients with eczema. An elimination diet is generally recommended for at least 6-12 weeks, during which highly reactive foods are eliminated from the patient's diet. During this time, the patient should focus on eating a nutrient-dense, anti-inflammatory diet emphasizing whole fruits, vegetables, omega-3 fatty acids, and fermented foods to reduce inflammation, support immune function, and promote a healthy gut microbiome. (8)

After the elimination phase, patients should begin to reintroduce IgG food sensitivities to challenge the patient's food tolerance and begin to expand dietary variety. Each reintroduction should be performed individually over three days, during which the patient should closely observe for any changes or exacerbations of eczema symptoms. Foods that do not elicit adverse reactions can be reincorporated into the diet, whereas foods that trigger eczema should continue to be avoided. (7

Supplements Protocol for Eczema

A combination of oral and topical supplements can be prescribed to reduce symptoms of eczema, treat dysbiosis and leaky gut, and regulate the immune system. 


Butyrate is a short-chain fatty acid known as the preferred fuel source of cells lining the small intestine, inhibiting inflammatory cytokines, and enforcing tight junctions. The severity of atopic dermatitis inversely correlates with the abundance of butyrate-producing microbiota. Therefore, supplemental butyrate can reduce intestinal permeability and modulate inflammatory immune responses.

Dose: one dose (per label) three times daily with meals 

Duration: 12 weeks

Virgin Coconut Oil

The emollient effect of coconut oil has been successfully demonstrated in patients with atopic dermatitis. Additionally, coconut oil has natural antimicrobial properties that support a healthy balance of the skin's healthy microbiome. One study showed that applying virgin coconut oil twice daily for one month resulted in a 95% eradication rate of Staph aureus for patients with atopic dermatitis. 

Dose: applied to the affected skin twice daily

Duration: 4 weeks, and continued as needed

*Note: Consider adding lavender or peppermint essential oils to the coconut oil for added anti-itch, anti-inflammatory, and antimicrobial properties.


L-histidine is essential for the synthesis of FLG and for regulating the skin's moisture content. Oral supplementation with L-histidine has resulted in a 34% reduction in atopic dermatitis severity and a 33% reduction in reported topical corticosteroid use by patients. (9

Dose: 2 grams twice daily

Duration: one month

Vitamin D

Lower serum vitamin D levels have been associated with a higher rate of bacterial skin infections, and vitamin D supplementation has been shown to reduce the clinical signs of eczema. (6)

Dose: 2,000 IU daily

Duration: 12 weeks

Light Therapy for Eczema

Phototherapy, also known as light therapy, is a treatment modality that utilizes specific wavelengths of light to manage eczema symptoms. Several types of phototherapy use UVA and UVB rays. Research shows that phototherapy effectively reduces inflammation, itching, and scaling associated with eczema. Phototherapy is considered safe, well-tolerated, and effective when administered 2-3 times weekly for 1-3 months. (11

When to Retest Labs

Clinical monitoring of symptoms is sufficient for many patients in monitoring treatment efficacy. Repeat labs may be warranted in some instances, such as needing to monitor nutrient deficiencies or confirm infection eradication. The frequency at which labs are repeated will vary individually, partly depending on clinical necessity and patient/doctor preference. If functional labs are going to be repeated, it is often recommended to retest at a 3-6 month interval to assess patient progress accurately.



In the quest for effective eczema treatment, a growing body of evidence supports the integration of conventional medicine with complementary and alternative therapies. This article explores the benefits of a functional medicine approach to correct imbalances impacting skin and gut health. The sample treatment protocol provides a framework for dietary and supplemental interventions specific to treating eczema that can be customized in clinical practice based on the patient's needs.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
Learn More
No items found.

Lab Tests in This Article

  1. Anderson, S. (2022, June 6). How to Talk to Your Patients About Leaky Gut: An Overview. Rupa Health.
  2. Buys, L.M. (2007). Treatment Options for Atopic Dermatitis. American Family Physician, 75(4), 523–528.
  3. Cleveland Clinic. (2017). Eczema. Cleveland Clinic.
  4. Cleveland Clinic. (2022). Atopic Dermatitis. Cleveland Clinic.
  5. Cloyd, J. (2023, March 8). Butyrate 101: Everything You Need to Know About This Short Chain Fatty Acid. Rupa Health.
  6. Cox, A.D. (2022, December 21). An Integrative Approach To Treating Eczema in Children. Rupa Health.
  7. Decesaris, L. (2022, August 30). How To Do An Elimination Diet. Rupa Health.
  8. Eczema elimination diet and foods to eat. (2020, January 2). Medical News Today.
  9. Gibbs, N.K. (2020). l-Histidine Supplementation in Adults and Young Children with Atopic Dermatitis (Eczema). The Journal of Nutrition, 150(Supplement_1), 2576S2579S.
  10. Greenan, S. (2021, December 3). 5 Ways To Treat Eczema Without Medication.
  11. Eczema: Light therapy and oral medications. (2019). In Institute for Quality and Efficiency in Health Care (IQWiG).
  12. Khakham, C. (2023, June 2). Top Evidence Based Herbal Medicine and Essential Oil Options for Skin Health and Healing. Rupa Health.
  13. Khakham, C. (2023, June 30). Personalizing Skin Health: Leveraging Functional Medicine Labs to Tailor Dietary Interventions and Supplements. Rupa Health.
  14. Mayo Clinic. (2020). Atopic dermatitis (eczema). Mayo Clinic.
  15. Morita, E., Hide, M., Yoneya, Y., Kannbe, M., Tanaka, A., & Yamamoto, S. (1999). An Assessment of the Role of Candida albicans Antigen in Atopic Dermatitis. The Journal of Dermatology, 26(5), 282–287.
  16. National Eczema Association. (2013). Eczema Stats. National Eczema Association.
  17. Nemeth, V., & Evans, J. (2020). Eczema. PubMed; StatPearls Publishing.
  18. Nylund, L., Nermes, M., Isolauri, E., et al. (2015). Severity of atopic disease inversely correlates with intestinal microbiota diversity and butyrate-producing bacteria. Allergy, 70(2), 241–244.
  19. Savolainen, J., Lammintausta, K., Kalimo, K., et al. (1993). Candida albicans and atopic dermatitis. Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology, 23(4), 332–339.
  20. Sweetnich, J. (2023, May 15). Integrative Dermatology Approaches to Seborrheic Dermatitis: Testing, Diagnosis, and Treatments. Rupa Health.
  21. Tauber, M., Balica, S., Hsu, C.-Y., et al. (2016). Staphylococcus aureus density on lesional and nonlesional skin is strongly associated with disease severity in atopic dermatitis. The Journal of Allergy and Clinical Immunology, 137(4), 1272-1274.e3.
  22. Varma, S.R., Sivaprakasam, T.O., Arumugam, et al. (2019). In vitro anti-inflammatory and skin protective properties of Virgin coconut oil. Journal of Traditional and Complementary Medicine, 9(1), 5–14.
  23. Verallo-Rowell, V.M., Dillague, K.M., & Syah-Tjundawan, B.S. (2008). Novel antibacterial and emollient effects of coconut and virgin olive oils in adult atopic dermatitis. Dermatitis: Contact, Atopic, Occupational, Drug, 19(6), 308–315.
  24. Yoshimura, H. (2023, June 7). The Gut Microbiomes Role in Skin Health. Rupa Health.
Subscribe to the Magazine for free to keep reading!
Subscribe for free to keep reading, If you are already subscribed, enter your email address to log back in.
Thanks for subscribing!
Oops! Something went wrong while submitting the form.
Are you a healthcare practitioner?
Thanks for subscribing!
Oops! Something went wrong while submitting the form.