The Hidden Nutrient Depletions Caused by Common Medications—and How They Impact Hormones, Mitochondrial Health, and Egg Quality

I recently completed a continuing education series in women's health. One lecture was about nutrient deficiencies caused by certain common medications. Much of this I knew, but what a great reminder to always start by replenishing nutrients that could be depleted by these medications when someone is feeling off.

In the United States, millions of people rely on everyday medications such as birth control pills, SSRIs, thyroid medication, and proton pump inhibitors (PPIs). These medications are often necessary and effective—but what many people don’t realize is that they can subtly deplete key nutrients over time. These nutrient shifts can influence everything from mitochondrial health to hormone balance, metabolism, and even oocyte quality, whether or not pregnancy is a goal.

This article explains:

• How medications contribute to nutrient depletion

• Which nutrients are most commonly affected

• Why the liver plays a central role

• How these shifts impact hormones, ovarian function, and overall vitality

• What you can do to restore these nutrients

This information is valuable for anyone looking to protect long-term metabolic and hormonal health.

How Medications Deplete Nutrients in the Body

Many medications are metabolized in the liver. During this process, they use up cofactors, increase oxidative stress, or alter the way nutrients are absorbed or activated. Over time, these mechanisms can lower nutrient stores in predictable ways.

Key pathways include:

1. Increased Liver Detoxification Demand

Medications often upregulate liver detox pathways—particularly cytochrome P450 enzymes. This process requires nutrient cofactors, including:

• B vitamins (B2, B6, B9, B12)

• Magnesium

• Glutathione

• Antioxidants like vitamin C and vitamin E

When the liver ramps up detoxification, it “burns through” nutrients faster than normal.

2. Altered Absorption in the Gut

Some medications change stomach acid, transit time, or microbiome composition. This affects absorption of:

• B12

• Iron

• Magnesium

• Zinc

• Fat-soluble vitamins

• Amino acids

3. Increased Oxidative Stress

Medications can directly or indirectly produce oxidative stress, especially in mitochondrial-rich tissues such as the liver, ovaries, and brain. This increases demand for:

• Antioxidants (vitamin C, E, glutathione)

• CoQ10

• Omega-3s

4. Interference With Nutrient Conversion

Some nutrients must be converted to active forms in the liver. Medications can hinder this process—leading to “functional deficiencies” even when blood levels look normal.

Nutrient Depletions by Medication Category

Below is a clinically grounded breakdown of nutrient depletions associated with some of the most commonly used medications in America.

1. Birth Control Pills (Combined Oral Contraceptives)

Oral contraceptives are among the most well-documented medications for nutrient depletion.

Nutrients Depleted by Birth Control:

• Folate (B9)

• B6

• B12

• Magnesium

• Zinc

• Vitamin C

• Vitamin E

• CoQ10 (mitochondrial)

How This Impacts Hormonal Health:

Mitochondria + Ovarian Function

The ovaries contain some of the highest mitochondrial concentrations in the body. Nutrient depletion—especially CoQ10, B vitamins, and magnesium—can impair:

• ATP production

• Steroid hormone synthesis

• Oocyte development

Even for individuals not trying to conceive, this can manifest as:

• PMS

• Fatigue

• Mood symptoms

• Low libido

• Cycle irregularity after discontinuation

Liver Detox Impacts

OCs increase hepatic workload, requiring additional nutrients for estrogen metabolism. When nutrients are low, estrogen clearance slows, contributing to:

• Estrogen dominance

• Breast tenderness

• Heavy or painful periods

• Migraines

2. SSRIs (Selective Serotonin Reuptake Inhibitors)

SSRIs do not “officially” deplete nutrients, but they are strongly associated with functional deficiencies.

Nutrients Impacted by SSRIs:

• Sodium (hyponatremia risk, especially in older adults)

• B vitamins (increased demand for B6, folate, B12 in neurotransmitter pathways)

• Magnesium (low levels worsen SSRI-related anxiety or insomnia)

• CoQ10 (mitochondrial oxidative stress)

• Vitamin D (correlated with SSRI response)

  
  

How This Affects Mitochondria & Hormones

SSRIs increase mitochondrial oxidative stress in certain brain regions and increase demand for methylation cofactors. When B vitamins or magnesium are low, individuals may experience:

• Fatigue

• Poor stress tolerance

• Slowed metabolism

• Sleep disturbance

  
  

These same nutrients also regulate hormone production and thyroid conversion, meaning depletion can indirectly influence:

• Progesterone production

• Cortisol balance

• Ovulatory quality

3. Thyroid Medication (Levothyroxine, T4)

Although thyroid medication does not directly deplete nutrients, it increases metabolic demand and requires certain nutrient cofactors for optimal function.

Nutrients Impacted by Thyroid Medication:

• Iron / Ferritin (needed for thyroid peroxidase)

• Selenium (conversion of T4 → T3)

• Zinc (thyroid receptor function)

• Magnesium (conversion and hormone sensitivity)

• Iodine (thyroid hormone synthesis)

• Vitamin A (receptor signaling)

  
  

How This Impacts Mitochondria & Hormone Function

Thyroid hormones regulate mitochondrial ATP production. When nutrients are insufficient:

• Conversion from T4 to active T3 slows

• Energy production decreases

• Ovarian cells (highly metabolic) make lower-quality oocytes

• Progesterone production dips

  
  

Even for non-fertility patients, this means:

• Fatigue

• Low libido

• Anovulation or long cycles

• Cold intolerance

• PMS or PMDD

4. Proton Pump Inhibitors (PPIs)

PPIs reduce stomach acid, which is essential for nutrient breakdown and absorption.

Nutrients Depleted by PPIs:

• Magnesium

• Vitamin B12

• Iron

• Calcium

• Vitamin C

• Protein absorption (secondary)

• Zinc (reduced gastric acidity impairs absorption)

  
  

Impact on Mitochondrial and Hormonal Health

Magnesium and B12 are essential for:

• ATP production

• DNA repair

• Ovarian follicle development

• Neurotransmitter synthesis

  
  

Low magnesium from chronic PPI use is strongly associated with:

• Anxiety

• Palpitations

• Sleep disturbances

• Muscle weakness

• Poor insulin sensitivity

  
  

Iron and B12 depletion—extremely common with long-term PPIs—can lead to:

• Fatigue

• Poor ovulation

• Temperature intolerance

• Hair thinning

• Low progesterone due to impaired ovarian energy production

Why Mitochondrial Health Matters for Hormones and Egg Quality

Mitochondria power almost every hormone-producing step in the body. In the ovaries, they:

• Provide ATP for oocyte maturation

• Control steroid hormone synthesis

• Regulate cell signaling for follicle development

Nutrient depletion → mitochondrial dysfunction → reduced hormone production and ovarian quality.

Symptoms of mitochondrial stress from nutrient depletion:

• Brain fog

• Fatigue

• PMS

• Low libido

• Long cycles

• Poor stress tolerance

• Mood instability

• Weight changes

This matters whether someone is planning pregnancy now, later, or never, because mitochondrial function drives overall metabolic and hormonal health.

How to Protect Yourself From Nutrient Depletion

Evidence-based strategies include:

• Targeted supplementation based on medication class

• Periodic nutrient testing (B12, ferritin, magnesium RBC, zinc, vitamin D, folate)

• Supporting liver detoxification with cruciferous vegetables, B vitamins, and antioxidants

• Eating nutrient-dense, whole-food meals with adequate protein

• Supporting the microbiome for better absorption

Final Thoughts

Medications like birth control, SSRIs, thyroid medications, and PPIs are widely used—and often necessary. But understanding the nutrient depletions associated with these drugs allows you to proactively support:

• Mitochondrial function

• Ovarian health and oocyte quality

• Hormone balance

• Mood stability

• Energy metabolism

Even if pregnancy is not the goal, protecting mitochondrial and hormonal health supports lifelong vitality, cognition, metabolism, and mood.

Several common prescription medications including birth control, SSRI’s proton pump inhibitors, thyroid medication deplete key nutrients in the liver

These nutrient deficiencies can negatively impact the mitochondrial health of the eggs in our ovaries 

When the mitochondria do not have the nutrients they need to function appropriately, hormone production suffers and can lead to hormone imbalances, unwanted symptoms and infertility. 

I am by no mans anti-medication in fact in my practice I lean on a combination of conventional medications and naturopathic treatments. However, we need to be talking about the impacts of these medications and support patients appropriately.