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Functional Medicine Protocol for Treatment of Acne

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Functional Medicine Protocol for Treatment of Acne

Acne is something we all experience at some point in our lives. It's frustrating, sometimes painful, and often impacts self-esteem, leaving us feeling insecure. Up to 95% of adolescents and 54% of adults over 25 struggle with acne. Whether it's mild and intermittent or severe and persistent, acne is a shared experience.

Acne has no specific cause, making it sometimes difficult to treat. Functional medicine, however, provides a beacon of hope for those that suffer from this condition. A functional medicine protocol for treating acne looks at all the potential factors that can contribute to this condition. It provides a targeted, unique plan to address the specific root cause.


What is Acne?

Acne, or acne vulgaris, is a common and uncomfortable skin condition that results from clogged hair follicles, which you may know as pimples or zits. Outbreaks of pimples most often affect the face, chest, shoulders, and back.

Tiny glands called sebaceous glands are attached to the hair follicles in the skin. These glands secrete sebum, an oily substance that keeps the skin moist and hydrated.

Sebum gets secreted onto the skin surface through an opening in the follicle called a pore. Typically, sebum is released, and dead skin cells are shed through the pore.

Sometimes hair, sebum, and dead skin cells clump together inside the pore, clogging the pore. Bacteria that live on the skin's surface begin to grow in the clogged pore, often causing inflammation, which can be painful.

Acne can affect anyone, but it affects females more than males and is most common in teens and young adults going through the hormone changes of adolescence.

Different Types of Acne

There are different types of acne. They are categorized as either inflammatory or noninflammatory.

The noninflammatory type of acne includes blackheads and whiteheads. Blackheads are referred to as open comedones because the top of the clogged pore remains open. Whiteheads are called closed comedones because the top of the clogged pore is closed.

The inflammatory type of acne includes papules, pustules, nodules, and cysts. Papules appear as small, tender red bumps. Pustules are papules that fill with pus. Nodules are large, solid, and often tender lumps deep under the skin. Cysts are deep, painful, pus-filled lumps.

What Causes Acne?

On a fundamental level, acne is caused by clogged hair follicles or pores. However, functional medicine seeks to identify a root cause and various environmental factors that can contribute to developing or worsening acne.


Genetics can affect acne. Studies show you're more likely to develop acne when there's a family history of acne.

Skin Microbiome Disruption

Just as there are trillions of microorganisms that live in the gut, which we call the gut microbiome, there are microorganisms that live on the skin, called the skin microbiome.

With an imbalance in the skin microbiome, acne can develop. This can result from tight-fitting clothing or hats, harsh skincare care products, and even antibiotic use. Acne is also associated with the skin colonization of a bacteria called Cutibacterium acnes (previously known as Propionibacterium acnes).


Hormone imbalance is a common cause of acne. Excess androgen hormones, such as testosterone, can trigger acne. This is why acne is a common symptom in conditions associated with high levels of androgen hormones, such as PCOS.

Significant fluctuations, or changes, in hormones, can also cause acne, such as during adolescence, pregnancy, postpartum, and menopause.

Increases in a hormone called insulin-like growth factor-1 (IGF-1) cause sebaceous gland growth and increased sebum production, which are associated with acne.

Food Sensitivities and Allergies

Certain foods are associated with acne. Dairy products and sugar are known to contribute to acne development, which may be due to the increase in IGF-1 that they cause.

Food allergies and sensitivities can also cause changes in the gut, such as dysbiosis and increased intestinal permeability (often called "leaky gut"), that can cause acne.

Micronutrient Imbalances

Imbalances in certain nutrients can cause acne. Low levels of zinc, vitamin A, vitamin E, and vitamin D, and high levels of vitamin B12 are associated with the development of acne.

Omega-3 and pantothenic acid (vitamin B5) supplementation were each shown to improve acne symptoms, indicating an association between these nutrients and acne.


The body's stress response causes a series of hormone interactions that involve the hypothalamic-pituitary-adrenal axis (HPA axis), including the release of the stress hormone cortisol.

The activation of the stress response can cause changes in the skin leading to various skin conditions, including acne. Stress also contributes to changes in the gut, such as leaky gut, that can cause acne.


Certain drugs can contribute to acne. This includes medications that contain testosterone, corticosteroids, or lithium.

Functional Medicine Labs to Test for Root Cause of Acne

Your functional medicine practitioner may order several lab tests to assess the root causes of your acne.

Hormone Testing

Hormone testing effectively determines whether increased androgen production, imbalances in other sex hormones, or imbalances in the HPA axis are causing your acne.

The DUTCH Complete is a urine test that can test sex hormones, adrenal hormones, and their metabolites, as well as a daily free cortisol pattern for a complete hormone and HPA axis assessment.

IGF-1 can be measured with a blood test to determine if the elevation of this hormone is contributing to your acne.

Micronutrients Testing

If micronutrient imbalances are the root cause of your acne, a Micronutrient Test is the best tool to identify which specific nutrients are a problem.

Vitamin D is also often tested with routine blood testing.

Comprehensive Stool Analysis

If imbalances in the gut are the root cause of your acne, a comprehensive stool test is a helpful way to uncover it. Stool testing evaluates gastrointestinal health in several ways, including digestion, absorption, inflammation, immune response, and the gut microbiome.

The Genova Diagnostics GI Effects® Comprehensive Profile also offers the ability to add on a zonulin test. Zonulin is a protein that can assess for increased gastrointestinal permeability or leaky gut.

Food Sensitivity Testing

Testing for food sensitivities will help identify whether an immune response to foods is contributing to your acne. The Cyrex Laboratories Array 10 is a blood test that evaluates immune reactivity to 180 different foods and additives.


Functional Medicine Treatment Protocol for Acne

A functional medicine treatment protocol for acne takes a whole-person, comprehensive approach. It looks at all potential environmental and lifestyle factors to identify a root cause to create an effective approach unique to each individual.

Since tight-fitting clothing and harsh personal care products can cause acne, avoiding these is a great starting point.

Therapeutic Diet and Nutrition Considerations for Acne

A nutritional approach for acne should include limiting or avoiding those foods known to contribute to the development of acne, such as dairy products and high-sugar foods.

If food sensitivities are suspected as a root cause of acne, an elimination diet is an important dietary consideration. An elimination diet can also be a helpful method for identifying food sensitivities if food sensitivity testing is not performed.

The elimination diet is a therapeutic diet in which suspected problematic foods are eliminated from the diet for a period of 3 to 4 weeks. After the elimination period, foods are reintroduced slowly and strategically under the guidance of your practitioner.

When foods are reintroduced, problematic foods are identified as they trigger symptoms, which can be immediate or delayed. The foods identified as being problematic and causing symptoms are eliminated for a period of 3 to 6 months before attempting to reintroduce them.

This approach can be enlightening in understanding how foods impact your health and can help uncover whether certain foods are causing your acne.

Supplements Protocol for Acne

Various supplements may be used in a functional medicine protocol for the treatment of acne, depending on each individual's root cause of acne. You should always follow the personalized recommendations of your functional medicine practitioner, who will determine the appropriate supplements and dosages for you.


L-glutamine is an amino acid significant for gut health as it provides the fuel source for the cells that line the gut. Factors such as stress and food sensitivities can cause damage to the gut lining, increased gut permeability (leaky gut), and inflammation, which can lead to acne. L-glutamine promotes healing of the gut lining, reduces intestinal permeability, and reduces inflammation in the gut.

L-Glutamine Recommendation

A commonly used strategy for L-glutamine is to take 5 grams three times per day on an empty stomach for eight weeks.


Cruciferous vegetables contain a plant compound called 3,3'-Diindolylmethane, or DIM, which has anti-androgenic properties. When excess androgen hormone production is identified as a root cause of acne, DIM is an excellent choice in the supplement protocol. In addition to its anti-androgen properties, evidence indicates DIM may also impact the skin microbiome. In this in vitro study, DIM displayed antimicrobial activity against several acne-causing bacteria, including Cutibacterium acnes.

DIM Recommendation

DIM is commonly recommended at 100 to 200 mg per day for 1 to 12 months.

DIM (diindolylmethane) may reduce the effectiveness of some medications, including birth control, so make sure to discuss it with your doctor before beginning any supplement.


Ashwagandha is a powerful adaptogenic herb. An adaptogen is a substance, most often an herb, used medicinally to help the body cope with and "adapt" to stress. Ashwagandha is celebrated for its ability to reduce cortisol, the stress hormone levels and support a healthy HPA axis. When stress and HPA axis dysfunction are identified as the root cause of acne, ashwagandha is a great option to support balance and manage stress.

Ashwagandha Recommendation

Ashwagandha is prescribed in doses of 225 to 600 mg per day and for up to 12 weeks.


When micronutrient deficiencies are indicated as a root cause of acne, a supplement like Designs for Health Acnutrol is an excellent addition to the supplement protocol. Acnutrol contains most of the micronutrients implicated as being deficient in acne or helpful for acne, such as zinc, vitamin A, vitamin E, vitamin D, and pantothenic acid.

Acnutrol Recommendation

The recommended use of the product is to take six capsules per day or follow your healthcare practitioner's directions.

Vitamin D

Vitamin D has several benefits for the body. In addition to being critical for bone health, vitamin D reduces inflammation and modulates glucose metabolism in the body. As discussed earlier, vitamin D deficiency is associated with acne. If a Micronutrients Panel or vitamin D test identifies vitamin D deficiency, it may be included in your acne supplement protocol.

Vitamin D Recommendation

To increase blood levels of Vitamin D back to normal, a "loading dose" is often required. A typical recommendation for loading dose is 50,000 IU once per week for 2 to 3 months or three times per week for one month. A maintenance dose of 800 to 2,000 IU per day is required to prevent a recurrence of deficiency.


Omega-3 fatty acids are vitally important to health and well-being. They are an essential component of cellular membrane structure; they benefit cardiovascular health, reduce inflammation, improve brain function, and are also shown to improve acne symptoms. Whether or not a Micronutrients Panel is performed and shows a deficiency of Omega-3s, they are an important part of a healthy lifestyle.

Omega-3 Recommendation

A standard recommendation for Omega-3 supplementation includes 2 grams per day for at least ten weeks.

When to Retest Labs

If food sensitivity testing was performed and sensitive foods were identified, re-testing is often performed after 3 to 6 months of avoiding that particular food.

It is recommended to wait 3 to 6 months to retest Vitamin D levels after beginning treatment with Vitamin D supplements.

The 3 to 6 months time frame is also ideal for retesting comprehensive stool analysis, sex hormones, and HPA axis to provide adequate time for the treatment protocol to improve the health of these systems.



Acne is a common, frustrating skin condition that many experience at some point, often significantly impacting self-esteem. Common causes of acne include hormone imbalance, nutrient imbalances, specific foods, food sensitivities, stress, imbalances in the microbiome, and medications.

Functional medicine treatment of acne takes a patient-centered approach, looking at all the potential factors that can contribute to this condition and providing a targeted, unique plan to address the specific root cause.

If you struggle with acne, talk to your functional medicine practitioner to uncover the underlying (root) causes of your skin condition and determine what treatment protocol is suitable for you.

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.
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