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June 26, 2025

Functional Medicine for Acne: Root Cause Treatments That Work

Acne is more than a skin issue—it’s a sign of deeper imbalances. Here’s how functional and integrative medicine help heal acne from the inside out.

Functional Medicine for Acne: Root Cause Treatments That Work

Root Cause Acne Treatment: A Functional Medicine Approach to Clear Skin Naturally

Understanding the biology of breakouts and how integrative care can heal skin from the inside out.

Introduction

Acne is often dismissed as a cosmetic nuisance, but for millions, it’s a painful and persistent condition that reflects underlying physiological imbalance. Topical creams and antibiotics may offer temporary relief, but breakouts often return until the root causes are addressed.

At its core, acne is an inflammatory skin condition, but its triggers lie deeper—in hormonal fluctuations, gut dysbiosis, insulin resistance, immune dysregulation, and toxin accumulation. Functional and integrative medicine approaches acne not as a surface-level issue, but as a systemic imbalance that manifests on the skin.

In this post, we’ll explore what really causes acne, how to uncover its triggers, and how a comprehensive, root-cause approach can help you achieve long-lasting clear skin—naturally.

What Is Acne?

Acne vulgaris is a chronic inflammatory condition of the pilosebaceous unit—the hair follicle and its associated oil gland. It leads to clogged pores, blackheads, whiteheads, cysts, and sometimes scarring.

Common Acne Types:

  • Comedonal acne: Whiteheads and blackheads

  • Inflammatory acne: Papules, pustules, and nodules

  • Cystic acne: Deep, painful, and prone to scarring

  • Hormonal acne: Often along the jawline, flares around menstrual cycles

Conventional Treatment: Why It Often Fails

Dermatology often treats acne with:

  • Topicals: Benzoyl peroxide, salicylic acid, retinoids

  • Antibiotics: Doxycycline, minocycline

  • Hormonal agents: Birth control, spironolactone

  • Isotretinoin (Accutane): For severe cystic acne

These can be helpful but often come with downsides:

  • Temporary relief

  • Rebound breakouts

  • Side effects: Gut issues, liver stress, mood swings

  • No investigation of root cause

Functional medicine asks a different question: Why is your body producing acne in the first place?

Functional Medicine: Looking Beneath the Surface

In functional medicine, we evaluate acne as a symptom of deeper imbalances. Skin is a reflection of internal health. If the gut, liver, hormones, or immune system are overwhelmed, the skin often pays the price.

Top Root Causes of Acne (and How to Address Them)

1. Hormonal Imbalances

Hormones are one of the most common root causes—especially in adult women.

Key Hormonal Triggers:

  • Androgens (testosterone, DHEA): Stimulate oil production

  • Insulin and IGF-1: Promote androgens and sebum

  • Estrogen/progesterone imbalance: Influences skin inflammation

  • Cortisol: Chronic stress promotes inflammation and sebum

Clues You May Have Hormonal Acne:

  • Flares before your period

  • Acne on jawline, chin, neck

  • Oily skin with irregular cycles

  • Acne + PCOS symptoms (hair loss, facial hair, weight gain)

Functional Testing:

Treatment Strategies:

For insulin resistance-related hormonal acne, retatrutide or tesamorelin may also help by restoring metabolic function.

2. Gut Dysbiosis & Leaky Gut

The gut-skin axis is real. Overgrowth of pathogenic bacteria or yeast can trigger systemic inflammation, which promotes acne.

Signs of Gut-Related Acne:

  • Bloating, constipation, or diarrhea

  • Food sensitivities

  • Brain fog or fatigue

  • Acne flares after antibiotics or sugary meals

Functional Testing:

Treatment Strategies:

Peptide option: LL-37 for antimicrobial immune support, particularly if acne is driven by microbial overgrowth or skin infections.

3. Insulin Resistance & High Glycemic Diet

Insulin triggers increased androgens and IGF-1, which fuel acne. Blood sugar spikes lead to more oil production and clogged pores.

Signs of Insulin Resistance:

  • Skin tags, dark patches (acanthosis)

  • Sugar cravings

  • Fatigue after meals

  • Midsection weight gain

Testing:

  • Fasting glucose, insulin

  • HOMA-IR calculation

  • Hemoglobin A1c

Treatment Strategies:

  • Low glycemic diet (limit sugar, dairy, refined carbs)

  • Time-restricted eating or fasting

  • Exercise (especially resistance training)

  • Support with:

Peptide options: CJC-1295 + Ipamorelin, Tesamorelin, and MOTS-c support metabolic health and insulin sensitivity.

4. Chronic Inflammation & Immune Dysregulation

Acne is fundamentally an inflammatory condition. Even non-hormonal or non-infectious acne reflects immune imbalance.

Triggers:

Testing:

Treatment Strategies:

Peptide option: KPV is a potent anti-inflammatory peptide shown to reduce cytokine activity, especially in skin-related inflammation.

5. Toxin Accumulation

Environmental toxins can burden the liver and impair detoxification of hormones and inflammatory byproducts.

Common Sources:

  • BPA (plastics)

  • Pesticides

  • Fragrance, parabens

  • Mycotoxins from mold exposure

Testing:

Treatment:

6. Skin Barrier Dysfunction

Acne-prone skin is often stripped of its natural oils by harsh topicals, which worsens irritation and promotes rebound oiliness.

Tips:

  • Avoid foaming cleansers and alcohol-based toners

  • Use non-comedogenic, pH-balanced moisturizers

  • Consider topical zinc, niacinamide, green tea extract

Functional Medicine Testing for Acne Patients

A comprehensive acne workup may include:

Test Purpose
HUMAP Sex & adrenal hormones
Gut Zoomer Gut dysbiosis and pathogens
Organic Acids Yeast, detox, nutrient status
Fasting insulin & glucose Metabolic function
Mycotoxins test Mold exposure
Food sensitivity panel Hidden immune triggers

Integrative Acne Treatment Timeline

Month 1–2:

  • Begin gut and hormone support

  • Identify and remove food/environmental triggers

  • Start peptides or key anti-inflammatory supplements

Month 3–4:

  • Optimize detox and blood sugar

  • Reintroduce clean skincare

  • Monitor symptom response and retest if needed

Month 5+:

  • Shift to maintenance

  • Support microbiome and hormonal rhythm

  • Consider peptides for immune support or scar repair

When Medications Make Sense

In some cases, medications may be helpful alongside a functional approach:

  • Spironolactone: For androgen-driven acne

  • Metformin: For PCOS with insulin resistance

  • Topical retinoids: To prevent pore clogging

  • Isotretinoin: For severe cystic acne unresponsive to all other therapies

Functional providers will always aim to minimize long-term pharmaceutical reliance, but occasionally integrate them strategically.

Final Thoughts: Treat the Root, Heal the Skin

Acne is not just a skin issue—it’s a systemic signal. When the root causes are addressed—whether hormonal, metabolic, microbial, or inflammatory—the skin begins to clear, and deeper health improves.

Functional and integrative medicine offers a sustainable, whole-body path to clear skin that is safe, effective, and aligned with optimal health.

Ready to Address Your Acne from the Inside Out?

We specialize in root cause acne treatment using personalized plans that may include supplements, peptides, testing, and more.

Book your consultation today to begin a journey to healthier skin—and a healthier you.

Scientific References

  1. Kurokawa I, et al. The role of hormones in the pathogenesis of acne vulgaris. J Dermatol. 2009.

  2. Bowe WP, Logan AC. Acne vulgaris, probiotics and the gut-brain-skin axis. Gut Pathog. 2011.

  3. Smith RN, et al. A low glycemic load diet improves symptoms in acne vulgaris patients: a randomized controlled trial. Am J Clin Nutr. 2007.

  4. Zouboulis CC, et al. Beyond the skin: how functional approaches improve acne therapy. Dermatoendocrinol. 2009.

  5. Santhanam S, et al. KPV peptide suppresses inflammation in experimental skin and colon models. Biochem Pharmacol. 2012.