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A Functional Medicine Menopause Protocol: Comprehensive Testing, Nutrition, and Supplements

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A Functional Medicine Menopause Protocol: Comprehensive Testing, Nutrition, and Supplements

Typically in a woman's 40s, she begins to experience the ovaries' slowed production of estrogen and progesterone, a transitional period called perimenopause. During this time, uncomfortable symptoms, such as hot flashes, night sweats, weight gain, and irregular periods, often occur. When a woman has experienced 12 consecutive months without a menstrual period, she has officially reached the end of perimenopause and transitioned into the menopausal phase of life.

An estimated 1.3 million women enter menopause annually in the United States. These hormonal shifts, often equated to a "second puberty," manifest physically, mentally, and emotionally. An integrative approach to hormonal support can ease this hormonal transition. This article will discuss what menopause is, lab tests that can help individualize treatment options and a sample functional medicine protocol that can be recommended to patients in clinical practice seeking menopausal support.


What is Menopause?

Menopause is the normal and permanent cessation of menses for one year that results from estrogen deficiency as ovarian function diminishes. Menopause is one point in a continuum of life stages for women that marks the end of their fertile years. After menopause, a woman cannot because pregnant naturally. The menopausal transition typically occurs gradually over many years, beginning with perimenopause, when menstrual cycle irregularities and other hormonal symptoms are first observed. (1-3)

Menopause Symptoms

In the months to years leading up to menopause, you may notice the appearance of menopausal-related symptoms, which most commonly include (2, 3):

  • Irregular and missed periods
  • Temperature fluctuations: hot flashes, chills, and night sweats
  • Vaginal dryness and discomfort during sexual intercourse
  • Low libido
  • Sleep disturbances
  • Changes in mood: irritability, mood swings, anxiety, depression
  • Weight gain
  • Thinning hair
  • Dry skin, eyes, and mouth
  • Breast changes: loss of fullness, tenderness
  • Urinary urgency and frequency

What Is the Usual Age for Menopause?

The average age of menopause for women in the United States is 51. The menopausal transition begins before this, usually in a woman's mid-40s. (4, 5)

About 5% of women experience early menopause between ages 40-45, and 1% of women experience premature menopause before age 40 due to premature ovarian insufficiency (4).

How Long Does Menopause Last?

Natural menopause occurs in three stages: perimenopause, menopause, and postmenopause. During perimenopause, the body begins to make less estrogen and progesterone. This hormonal decline occurs rapidly during the last one or two years of perimenopause. Perimenopause can last from months to ten years, although the average duration is four years. Once a woman hasn't had a period for 12 consecutive months, it is determined that she has reached menopause. After this, she enters the postmenopausal stage. (6)

Functional Medicine Labs That Can Help Individualize Treatment for Menopause Symptoms

Diagnostic labs are not required to diagnose menopause. However, they can help get to the root of menopausal symptoms and to individualize treatment plans. Below are some of the most common functional labs ordered for women experiencing menopausal symptoms.

Comprehensive Hormone Panel

Hormone analysis can be performed through blood, urine, and salivary testing. Common lab panels ordered by functional medicine providers include the urinary DUTCH Complete and serum Female Hormone Panel. The DUTCH test measures metabolites of hormonal pathways to assess reproductive hormones, cortisol, organic acids, and oxidative stress. A serum panel includes all the major female hormones, including estradiol, testosterone, progesterone, FSH, and LH. Elevations in FSH and LH with decreased levels of estrogen and progesterone are typical serum lab findings indicative of menopause.

Thyroid Panel

Subclinical and overt thyroid dysfunction can present with similar symptoms to menopause. Additionally, the incidence of thyroid dysfunction increases during the perimenopausal and menopausal periods. Therefore, including a thyroid panel on your lab order aids in a holistic and complete women's health evaluation.

Comprehensive Stool Test

Evidence demonstrates reduced gut microbiota diversity and increased intestinal permeability in postmenopausal women compared to premenopausal women (3). Using a comprehensive stool test to analyze the gut microbiome and measure zonulin, a marker of leaky gut, can help personalize gut-specific treatment recommendations to support gastrointestinal function during the stages of menopause.

Cardiometabolic Assessment

Distinct changes in lipid levels, including elevated total cholesterol, LDL cholesterol, triglycerides, and lipoprotein(a), have been documented in menopausal women (2). This, in part, contributes to the increased risk of heart disease observed in women during the menopausal stage of life (5). A lipid panel can track changes in lipid markers as a woman proceeds through the menopausal transition.

Variations in glucose metabolism and liver function can contribute to weight gain, hormonal imbalances, and cholesterol shifts. A comprehensive metabolic panel (CMP) can monitor changes in insulin sensitivity, glucose levels, and liver function.


Conventional Treatment for Menopause

Hormone replacement therapy (HRT), through systemic hormone therapy or low-dose vaginal products, is the most common conventional treatment for menopausal symptom management. Systemic HRT uses estrogen, progesterone, and/or testosterone in various forms, such as pills, patches, rings, gels, creams, or sprays, to manage systemic symptoms of menopause. Vaginal products provide local estrogen to the vagina in a cream, tablet, or ring form to manage vaginal and urinary menopausal symptoms. Although considered a conventional treatment option, many functional providers are trained in and incorporate HRT into their practices. (7, 8)

Non hormonal options are also available to manage physical and emotional menopausal symptoms, such as low-dose selective serotonin reuptake inhibitor (SSRI) antidepressants, gabapentin, pregabalin, and vaginal moisturizers. (7, 8)

Functional Medicine Treatment Protocol for Menopause

Dietary and lifestyle modifications can be highly beneficial in easing the menopausal transition and reducing symptoms. Healthy nutrition and lifestyle habits can significantly relieve symptoms, with or without conventional or alternative hormone support.

Therapeutic Diet and Nutrition Considerations for Menopause

A nutritious, whole-food diet can reduce inflammation, support a healthy gut microbiome, and prevent disease. Adopting a perimenopause diet as you begin to experience perimenopause can ease the transition into menopause.

Foods that improve hormonal symptoms in menopausal women include fruits and vegetables, phytoestrogen-containing foods, and unsaturated fats. Fruits and vegetables are packed with essential micronutrients and fiber that support whole-body wellness, assist adrenal and thyroid function, and support hormone balancing. Phytoestrogens in soy, whole grains, cruciferous vegetables, red clover, and legumes weakly bind estrogen receptors to reduce estrogen-deficiency-associated symptoms without serious side effects. Omega-3 fatty acids, highly concentrated in fatty fish and flax seeds, possess anti-inflammatory properties that improve hot flashes, uplift mood, and prevent cardiovascular disease. (9, 10)

Refined sugars, processed foods, spicy foods, alcohol, and caffeine can contribute to menopausal symptoms and should be reduced or avoided in the diet (9, 11).

Supplements Protocol for Menopause

Many botanical products have been used for centuries to treat menopausal symptoms naturally. Below is a sample protocol consisting of popular supplements recommended by functional medicine doctors to address common menopausal symptoms naturally.

Women's Phase II

Women's Phase II is a botanical formula containing Dong Quai, licorice root, wild yam, burdock root, and motherwort. These phytoestrogenic herbs support breast, bone, heart, uterine, and liver tissues. Used in a small double-blind, placebo-controlled study, 71% of the women taking this formula reported fewer total symptoms, and 100% had a reduction in the severity of their menopausal symptoms.

Dose: 2 capsules 2-3 times daily

Duration: at least three months

Black Cohosh

Evidence has demonstrated positive effects, comparable to low-dose transdermal estrogen therapy, in managing hot flashes, night sweats, and psychological symptoms of menopause with supplemental black cohosh (12, 13).

Dose: 40-128 mg daily, in split doses

Duration: up to 12 months

Femmenessence MacaPause

Maca root is an adaptogenic herb used for thousands of years to help the body adapt to stress, support cognitive function, and improve libido. Clinical research supports using maca-containing MacaPause to treat menopausal symptoms of hot flashes, night sweats, mood swings, and low libido.

Dose: 2 capsules twice daily (before breakfast and between 12-3pm)

Duration: at least three months

When to Retest Labs

Patients initiating HRT should have hormones monitored monthly until hormonal ranges are within an optimal range. Once the patient has reached a therapeutic and consistent HRT dosing regimen with stable symptoms, retesting can be decreased to every 6-12 months.

While herbal therapies can be just as effective as HRT, the time to see their maximum effect is generally longer. Patients managing menopausal symptoms with natural supplements, therefore, should expect to have labs retested in 3-6 month increments.



Menopause is a natural part of a woman's life. For many women, this transition to their post-fertile years can be rocky, accompanied by many uncomfortable symptoms that present new challenges. However, it doesn't need to be this way. Many options can minimize menopausal symptoms, making the transition manageable. Working with a functional medicine provider, you can determine the best and safest options to incorporate into a holistic treatment plan.

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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Lab Tests in This Article

1. World Health Organization. (2022, October 17). Menopause. World Health Organization.

2. Preston, J. (2023, March 15). An Integrative Medicine Approach to Managing Menopause Symptoms. Rupa Health.

3. Christie, J. (2023, January 31). 5 Functional Medicine Lab Tests To Consider For Women in Menopause. Rupa Health.

4. Peacock, K., & Ketvertis, K. M. (2018). Menopause. PubMed; StatPearls Publishing.

5. Cleveland Clinic. (2021). Perimenopause: Age, Stages, Signs, Symptoms & Treatment. Cleveland Clinic.

6. National Institute on Aging. (2017). What Is Menopause? National Institute on Aging.

7. Menopause treatments. (2017, July 12). Office on Women's Health.

8. Hill, D.A., Crider, M., & Hill, S.R. (2016). Hormone Therapy and Other Treatments for Symptoms of Menopause. American Family Physician, 94(11), 884–889.

9. Conner, V. (2022, August 2). Nutrition and Lifestyle Tips to Help Reduce Hot Flashes. Rupa Health.

10. Cloyd, J. (2023, May 26). A Functional Medicine Perimenopausal Protocol: Specialty Testing, Therapeutic Nutrition, and Supplements. Rupa Health.

11. Christie, J. (2023, January 10). How to Build a Personalized Nutrition Plan for Your Perimenopausal Patients. Rupa Health.

12. Kronenberg, F. (2002). Complementary and Alternative Medicine for Menopausal Symptoms: A Review of Randomized, Controlled Trials. Annals of Internal Medicine, 137(10), 805.

13. Nappi, R.E., Malavasi, B., Brundu, B., et al. (2005). Efficacy of Cimicifuga racemosa on climacteric complaints: A randomized study versus low-dose transdermal estradiol. Gynecological Endocrinology, 20(1), 30–35.

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