Your Complete Functional Medicine Guide To Natural Hormone Balance


How do Hormones Work?

Think of your hormones like chemical messengers of your body. Each hormone sends specific instructions to every organ, making hormones responsible for just about everything your body does – how it works, how it feels, and how healthy it is. Hormones influence your mood, energy level, weight, temperature, digestion, and many other aspects of your health. And yet, we don’t often think about, let alone appreciate, our hormones until they stop working the way we want them to. And when that happens, because of their wide influence, we definitely notice.

Your hormones are produced in the major endocrine glands – your brain (hypothalamus, pineal, and pituitary glands), thyroid, parathyroid, adrenals, pancreas, and reproductive glands (ovaries and testes). Some hormones are also produced in your gastrointestinal tract. With hormones, it’s all about balance. As Goldilocks lamented (and I’m paraphrasing here), there can’t be too much or too little. Hormones have to be just right. Otherwise, a myriad of health issues can happen.

How is a hormone imbalance diagnosed?

When you suspect hormone imbalance, mainstream medicine typically runs only basic labs. If your labs don’t come back “normal,” you’re typically given a synthetic hormone cream or pill that could have side effects. If those labs come back “normal” and you’re still experiencing symptoms, you may be told you’re either depressed, just getting older, or need to lose weight. However, there may just be some underlying issues, which in functional medicine we aim to get to the bottom of so you can eliminate the problem at it’s source. 

What causes hormone imbalance?

In functional medicine we aim to find out the root cause of patients’ hormonal symptoms as well as support the body’s natural mechanisms for healthy hormone balance. Doesn’t that make a lot more sense?

There can be many underlying causes of hormone imbalance including:

What are the symptoms of Hormone Imbalance?

Hormone imbalances differ in symptoms, diagnosis, and treatment depending on which specific hormones your body is struggling to maintain proper levels of. Let’s go over some of the most common hormone health problems that I see in patients, and that you may be going through right now. I’ll also explain which labs you may want to consider asking your doctor about. 

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 Common hormone health problems + their symptoms

 1. Cortisol

Our adrenal glands secret several hormones, and one of them is cortisol, your body’s primary stress hormone. Adrenal fatigue happens when there’s an imbalance in this cortisol rhythm: Cortisol is high when it should be low, low when it should be high, or always high or always low. Adrenal fatigue is really a dysfunction of your brain’s communication with your adrenals – not the adrenal glands themselves. Because adrenal fatigue is mainly a brain stress problem, the functional medicine solution focuses on minimizing chronic stressors.

What you might experience:

  • Trouble getting started in the morning
  • Craving salty or sugary foods
  • Low sex drive
  • Fatigued in the afternoon but you get a “second wind” in the evening
  • Trouble staying asleep at night
  • Dizziness after standing up too quickly
  • Afternoon headaches
  • Blood sugar issues
  • Chronic inflammation
  • Weak nails and brittle hair
  • Moodiness
  • Trouble losing weight

The Labs: I run a 24-Hour Adrenal Stress Index, a salivary test that tracks your cortisol levels, and an HPA (brain-adrenal) axis quality lab.

     2. Thyroid

Every cell of your body needs thyroid hormones to function optimally. There are many underlying thyroid problems that won’t show up on standard labs. For example: thyroid conversion issues, thyroid resistance, or autoimmune attacks against the thyroid (Hashimoto’s or Graves’ disease).

What you might experience:

  • Feeling tired
  • Cold feet, hands, or cold all over
  • Requiring extra sleep to function properly
  • Rapid weight gain
  • Constipation
  • Depressed or lack of motivation
  • Morning headaches that subside as the day goes on
  • Thinning of the outer third of eyebrows
  • Excessive hair loss or thinning
  • Dry skin
  • Brain fog

The Labs: Mainstream medicine typically just runs TSH and T4 (inactive thyroid hormone) to determine thyroid hormone dosage. A functional medicine thyroid panel involves looking at many other labs such as Free and Total T3 (active thyroid hormone), Reverse T3, and thyroid antibodies to rule out autoimmune thyroid problems. For a full list of thyroid labs and how to interpret them, read my previous article here.

     3. Estrogen

The ratio of the three forms of estrogen – estrone (E1), estradiol (E2), estriol (E3) – is important for both women and men. Some research has linked imbalances in estrogens to increased mortality rates in those with heart disease (1) as well as the progression of some cancers. (2)

What you might experience with low estrogen:

  • Vaginal dryness
  • Night sweats
  • Brain fog
  • Recurrent bladder infections
  • Feeling lethargic
  • Depression
  • Hot flashes

What you might experience with high estrogen:

  • Bloating
  • Rapid weight gain
  • Breast tenderness
  • Mood swings
  • Heavy menstrual bleeding
  • Anxiety
  • Depression
  • Migraine headaches
  • Cervical dysplasia (abnormal pap smear)
  • Insomnia
  • Brain fog
  • Gallbladder problems

The Labs: A full blood and salivary female hormone panel, including all estrogen isomers, can shed light on the specific problem.

     4. Progesterone

Both men and women need healthy progesterone balance. Progesterone helps balance and neutralize the effects of too much estrogen. Without proper progesterone levels, estrogen becomes out of control, also known as estrogen dominance.

What you might experience:

  • PMS
  • Insomnia
  • Poor complexion
  • Painful breasts
  • Stubborn weight gain
  • Cyclical headaches
  • Anxiety
  • Infertility

The Labs: A full blood and salivary female hormone panel.

     5. Testosterone

I often see low testosterone in both men and women in my functional medicine clinic. Studies have linked low testosterone in women to heart disease, low sex drive, (3) and breast cancer. (4) One study (5) found that men with low testosterone had a great rate of death. But you can also have too much.

What women might experience with excess testosterone:

  • Acne
  • Polycystic ovary syndrome (PCOS)
  • Excessive hair on the face and arms
  • Hypoglycemia and/or unstable blood sugar
  • Thinning hair
  • Infertility
  • Ovarian cysts
  • Mid cycle pain/cramping
  • Irritability

What women might experience with low testosterone:

  • Weight gain
  • Fatigue
  • Low sex drive

What men might experience:

I often see the over-conversion of testosterone to estrogen in men. Men don’t produce estrogen like women but convert it through a process called aromatization. Excess activity of the enzyme aromatase can cause low testosterone and high estrogen in men resulting in:

  • Erectile dysfunction
  • Low sex drive
  • Weight gain
  • Irritability
  • Breast enlargement

The Labs: Blood and saliva testosterone and DHEA panel.

     6. Leptin

Your fat cells aren’t just some unsightly nuisances that jiggle and make clothes not fit; they’re actually an intelligent part of your endocrine (hormonal) system. Fat cells produce a hormone called leptin.

One of leptin’s jobs is to tell your brain to use the body’s fat stores for energy. Leptin resistance occurs when your body – specifically your hypothalamus in your brain – stops recognizing leptin. This can trick your brain into thinking you are starving, resulting in excessive and inappropriate fat storage.

What you might experience:

  • Rapid weight gain
  • Weight loss resistance
  • Frequent strong food cravings
  • High stress levels

The Labs: Serum leptin.

     7. Insulin

Just like leptin resistance, insulin resistance is not a hormonal deficiency but a hormonal resistance pattern. Most people know insulin resistance when it comes to type 2 diabetes, but insulin resistance can also happen in those who are pre-diabetic, or have subclinical blood sugar imbalance.

This pre-diabetic metabolic syndrome is marked by this resistance to insulin meaning your body is producing insulin but the insulin is not doing what it should, i.e., shuttling blood sugar into your cells where you can use it. Instead, this ineffective insulin, through a cascade of reactions, results in excessive fat storage, making weight loss seem impossible.

What you might experience:

  • Cravings for sweets
  • Irritability or lightheadedness if you miss a meal
  • Dependence on coffee
  • Shaky, jittery, or tremors
  • Feeling uncharacteristically agitated, upset, or nervous
  • Poor memory
  • Blurred vision
  • Fatigue after eating
  • Sugar cravings
  • Waist girth equal to or larger than hip girth
  • Frequent urination
  • Increased thirst or appetite
  • Weight loss resistance

The Labs: Serum insulin, c-peptide, fasting blood sugar, and HbA1c.

How can I balance my hormones naturally?

Because all the systems in the body are interconnected, if you have one hormone problem, you might have other ones as well. In other words, to say you have only one of these seven issues might be oversimplification – it could be all of these issues or a combination of some of these. It’s important to work with your health care provider to find out what hormone issues might actually be at play, in order to create a safe and effective natural hormone balance treatment plan

Recently, I’ve been working on rehabbing my own adrenal fatigue and have shared my journey to natural hormonal balance in my 90-day hormone reset.

When it comes to attempting natural hormone balance, there are some important factors in play that you can focus on first, specifically your diet. 

The Best Hormone-Balancing Diets Ranked By A Functional Medicine Expert

When looking for a place to start rehabbing hormone health and addressing hormones and weight gain, many people often turn to the internet for answers. While the internet is a great resource, there can be a lot of often conflicting information on the best diets to heal chronic health problems. We have to remember that what works for one person doesn’t always work for another even when two people have the same diagnoses. However, there are a few specific eating styles that often work very well for hormone imbalances in particular. Take a look for my definitive ranking of the best hormone balancing diets based on the latest research and my clinical experience:

     1. AIP

This acronym stands for the Autoimmune Protocol and it is my number one when it comes to treating autoimmune based hormone problems such as autoimmune-thyroid problems like Hashimoto’s disease.

Autoimmune conditions occur when a genetic weakness is triggered by an autoimmune system response to certain foods, viruses, or toxins, which all contribute to chronic inflammation.

An AIP diet takes out all potential inflammatory foods and is more strict than a paleo diet. It eliminates everything that a paleo diet does with the addition of eggs, chocolate, nuts and seeds, and nightshades like tomatoes and peppers. These foods tend to elicit inflammation in people with autoimmune problems.

     2. Ketogenic diet

In the health community, the ketogenic diet is considered the new kid on the block. Even though it has been used for years as a natural treatment for children with epilepsy, it is gaining popularity for its ability to restore energy, fight inflammation, and regulate hormones.

This diet is high fat, low carb, and moderate protein. Every person has different daily calorie intakes and a specific ratio of fat, protein, and carbs that they must meet every day depending on your individual weight and health goals.

The goal of this diet is to reach ketosis. This is a state where your body uses ketones instead of glucose for energy. When your body no longer has a glucose source the body uses fat to produce ketones. Our bodies have always relied on fat for fuel from a biological (14) and evolutionary (15) perspective. Babies rely on fat from breast milk for brain growth and development. In fact, your brain is made of 60% fat!

Many studies have shown a ketogenic diet to be beneficial in managing blood sugar and controlling metabolism due to its focus on fat. And by feeding your brain fat it helps alleviate adrenal fatigue (HPA-axis dysfunction).

The wonderful thing about a ketogenic diet is that it can be done along with whatever other diet you are currently doing. It doesn’t matter what foods you are eliminating, you just calculate your ratios and meal plan around the foods you are allowed to eat. By nature, a ketogenic diet already takes out sugar, high-fructose fruits, and grains but even those following an AIP diet can thrive on this high-fat diet.

     3. Paleo

For those just starting to eat healthier, a paleo diet is a great place to start. It is less strict than AIP and other healing tools like a ketogenic diet or intermittent fasting can easily be added into this eating style.

Inflammatory foods like sugar and grains are eliminated with the addition of legumes. Beans contain phytate and lectin proteins which can contribute to digestive issues and lead to increased inflammation which can continue to feed hormone problems.

     4. Intermittent fasting

Just like a ketogenic diet, intermittent fasting can easily be incorporated into any of these above diets. In my functional medicine clinic I often use different IF protocols to heal both hormone and gut health issues, and overall to reduce inflammation. While intermittent fasting can be an amazing tool, it can cause some potential side effects for those dealing with hormone imbalances – thyroid problems, and adrenal fatigue (HPA-axis dysfunction) in particular.

For people with adrenal fatigue, I’ve found that intermittent fasting isn’t always the best choice when treating circadian rhythm dysfunctions. Women can also be more sensitive to IF because they have a higher amount of the protein kisspeptin which can contribute to menstrual irregularity, poor metabolism, and infertility. Not to say that intermittent fasting is completely out of the question for those with these specific hormone imbalances, but it may require a lot more modification and monitoring.

However, intermittent fasting takes center stage when it comes to healing insulin resistance. Studies have linked (13) intermittent fasting with increased metabolism and lower insulin resistance. (14) Make sure to still work with your doctor to monitor your progress as your glucose stabilizes.

And if you thought you’d have to worry about hunger while intermittent fasting, think again! Fasting actually positively affects your hunger hormone, ghrelin which improves brain dopamine levels. (16) Just one more example of the gut-brain axis connection!

What can I drink to balance my hormones?

These three elixirs are among my favorite tools to achieve natural hormone balance: one for thyroid, one for adrenal, and one for sex hormone health. Drink up and heal your hormones!

Thyroid Booster Smoothie


  • 1 cup full-fat coconut milk
  • 1 cup mixed greens
  • 1 cup organic frozen berries
  • 1 avocado
  • 1 stick of celery
  • 1 scoop collagen protein
  • 2 tablespoons dulse flakes
  • 1 tablespoon maca powder
  • 1 tablespoon extra-virgin coconut oil
  • 2 Brazil nuts


Blend all ingredients in blender.

What’s it doing? To improve health you need healthy fats, so bring on the coconut milk, oil, and avocados. Green leafy vegetables facilitate healthy methylation, which we all need for healthy hormone production. Brazil nuts are packed with selenium, which your body uses to make the enzyme (5′ deiodinase) to convert your inactive thyroid hormone T4 into the active T3. Seaweeds like dulse flakes are rich in iodine, which is the raw material for making thyroid hormone. Maca powder helps to stabilize hormone levels, and celery is a great food medicine for healing the gut, which is also needed for optimal thyroid hormone levels.

Sex Hormone Boosting Elixir


  • 2 cups full-fat coconut milk
  • 1 teaspoon cacao powder
  • 1 teaspoon shilajit powder
  • 1 teaspoon mucuna pruriens powder
  • 1 teaspoon raw honey
  • 1/2 teaspoon cinnamon


  1. Blend ingredients well in a blender.
  2. Pour into a saucepan and heat for 3 to 5 minutes over medium heat until warm.

What’s it doing for me? In addition to the hormone-building healthy fats of coconut milk, cacao, shilajit, and mucuna pruriens have all been traditionally used to balance sex hormones – estrogen, progesterone, and testosterone –  and serve as potent aphrodisiacs. Enjoy!

Refreshing Adrenal Balancing Iced Tea


  • 1 teaspoon ashwagandha powder
  • 1 teaspoon rhodiola powder
  • 1 teaspoon holy basil powder
  • 1 teaspoon cinnamon


  1. Pour 1 to 2 cups of hot water over herbs.
  2. Let steep for 15 minutes.
  3. Pour over ice.

How to make the most of these superfood drinks

You can give your body the best foods in the world, but if your day is filled with stress, you will be sabotaging your efforts at hormone health. Amplify the power and purpose of these three drinks by creating a ritual of serenity around drinking them. Find a quiet time in your day, maybe before the day starts in the morning or in the afternoon when you get home. Turn off your phone, dim the lights, close the door, and be silent and calm as you sip on any of these nourishing beverages. By bringing mindfulness to this practice, you will nourish your soul as well as your body. Also, because your hormones all influence one another, be holistic and try all three, rotating one per day throughout the week.

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  2. Giton F, de la Taille A, Allory Y, et al. Estrone sulfate (E1S), a prognosis marker for tumor aggressiveness in prostate cancer (PCa). J Steroid Biochem Mol Biol. 2008;109(1-2):158‐167. doi:10.1016/j.jsbmb.2007.10.005
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Dr. Will Cole, DNM, IFMCP, DC is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian, The Inflammation Spectrum and the brand new book Gut Feelings: Healing the Shame-Fueled Relationship Between What You Eat and How You Feel.

Gut Feelings Dr. Will Cole 6

Gut Feelings

Healing The Shame-Fueled Relationship
Between What You Eat And How You Feel