Hormonal birth control can deplete key essential nutrients like B6, B12, magnesium, and folate. Learn what’s happening in your body, why it matters, and how to restore balance when food is not enough.

Many women experience fatigue, mood swings, PMS, or low energy while on hormonal birth control—yet these symptoms are often brushed off. What’s less known is that contraceptives like the pill can quietly deplete your body of key nutrients critical for mood, metabolism, and hormone balance. In this guide, you'll learn why this happens, which nutrients are most affected, and exactly how to support your body before, during, and after hormonal birth control use.

How Hormonal Birth Control Affects Nutrient Levels

Few people know that popular hormonal methods of contraception, including pills, patches, rings and implants, are not as harmless and selfless to our bodies as they seem. They regulate ovulation and prevent pregnancy by replacing our hormones with their synthetic forms (oestrogen and progestin).

These synthetic hormones completely integrate into our metabolism, creating an additional burden on metabolic systems (liver, intestines, cells) and increasing the need for key nutrients.

New research shows that oral contraceptives can disrupt the barrier function of the gut, contributing to increased intestinal permeability, often referred to as ‘leaky gut syndrome.’ Synthetic oestrogens and progestins can alter the gut microbiota, reduce microbial diversity, and weaken the tight junctions in the intestinal mucosa. This disruption can lead to inflammation, bloating, food sensitivities, and poor nutrient absorption.

Synthetic oestrogens and progestins can cause stress to the mitochondria — the energy centres of our cells — amplifying the body's need for B vitamins, magnesium and antioxidants. When these needs are not met, symptoms similar to mental or hormonal disorders may appear. Depression, anxiety, poor skin condition and decreased libido may be related not only to hormones but also to nutrient depletion.

Even a small but steadily increasing chronic nutrient deficiency, especially of vitamins B6, B12, folate, magnesium and zinc, can lead to a so-called ‘hidden’ or ‘silent’ deficiency, which manifests itself in the form of fatigue, mood swings, restlessness, anxiety, loss of libido and skin problems.

The FDA-approved labelling for oral contraceptives acknowledges that oestrogen-containing contraceptives can lower levels of folic acid, vitamins B6 and B12. However, any nutrient deficiencies are rarely discussed in the context of hormone therapy. Let's reframe the symptoms associated with artificial hormone use as potential signs of key micronutrient depletion and talk about how to find safe and effective strategies for your long-term well-being and individual approach to reproductive health.

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5 The Top Deficiencies You Can’t Ignore

1. Vitamin B6 (also called P-5-P)

Vitamin B6 helps your body make important brain chemicals that control your mood, focus, and sleep.

Birth control hormones can lower your vitamin B6 levels in two ways: they make you lose more B6 through urine, and they make it harder for your body to use the B6 you get from food and basic supplements.

When you don't have enough active form of B6, you might feel irritable, anxious, or down, or have worse PMS. Many people don't realise these feelings can be linked to low active B6 from taking birth control.

The best way to fix this is to take vitamin B6 in its ready-to-use form, called P-5-P (pyridoxal-5-phosphate).

Regular vitamin B6 supplements need to be converted by your liver before your body can use them. But P-5-P is already in the right form, which is especially helpful since birth control puts extra work on your liver.

Getting enough P-5-P can help improve your mood, reduce PMS symptoms, and keep your nervous system healthy. This is why it's so important for anyone taking birth control.

💡That's why our supplement uses a biologically active form of B6 that your body can use right away.

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2. Vitamin B12 (methylcobalamin)

Vitamin B12 helps keep your energy up, your mind sharp, and your blood healthy. But if you're on birth control pills or other hormonal contraceptives, your body may have trouble absorbing this important vitamin from your food.

When you don't get enough B12, you might start feeling tired all the time, have trouble thinking, feel down, or notice tingling in your hands and feet. These problems can develop slowly over time.

If you use birth control, look for vitamin B12 supplements that say “methylcobalamin” on the label. This form is easier for your body to use than regular B12 (cyanocobalamin) because your liver doesn't need to process it first.

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3. Folate (L-5-MTHF)

Folate plays a crucial role in methylation (a key detoxification process), DNA synthesis and repair, mood regulation, and fertility. It's vital if you are thinking about a healthy pregnancy since folate deficiency can cause neural tube defects in the baby. Hormonal contraceptives—especially combined ones—reduce folate levels by both impairing absorption and increasing the body's need for it. This is particularly concerning since many people have genetic variations (like MTHFR mutations) that make it difficult to convert synthetic folic acid into the biologically active form their body needs.

That's why supplements containing L-5-MTHF—the natural, biologically active form of folate—are essential for women taking hormonal contraceptives. This form doesn't need conversion and is absorbed better in the body. Using L-5-MTHF helps restore folate levels, supporting healthy methylation pathways, mood, energy levels, and fertility.

💡That's why we chose the methylated form of folate instead of synthetic folic acid

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4. Magnesium (glycinate or malate)

Magnesium is a vital mineral that your body requires for numerous essential functions. It helps your muscles, nerves, blood sugar levels, hormones, and how you handle stress.

If you take birth control pills, paying attention to magnesium is extra important. Research shows that birth control makes your body lose more magnesium through urine. When you don't have enough magnesium, you might feel tired, get muscle cramps, have trouble sleeping, feel anxious, or have worse PMS symptoms.

There are two helpful types of magnesium supplements: magnesium glycinate and magnesium malate. Magnesium glycinate is beneficial for promoting a sense of calmness and improved sleep, particularly when you're experiencing stress or irritability. Magnesium malate helps boost your energy. Taking either type can help you sleep better, improve your mood, and make your periods easier to handle, which is especially helpful if you're dealing with hormone changes from birth control.

💡Adding magnesium can improve PMS, sleep and energy.

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5. Zinc (picolinate or bisglycinate)

Zinc is a mineral that your body needs for many important things. It helps keep your immune system strong, heals your skin, and supports your reproductive health. Even though birth control pills change your natural hormone levels, getting enough zinc is still very important, especially for keeping your skin healthy, fighting off infections, and helping your body return to normal after stopping the pill.

After you stop taking birth control pills, your body needs good zinc levels to start making hormones normally again. Without enough zinc, you might notice:

• Ongoing acne problems
• Cuts and scrapes that take longer to heal
• Getting sick more often
• Less interest in sex

Many people think these problems are just because of hormone changes, but they can actually be signs that you need more zinc. The best types of zinc supplements are zinc picolinate and zinc bisglycinate. These forms are easier for your body to absorb and won't upset your stomach. Getting enough zinc can help clear your skin, boost your immune system, improve your mood, and support your reproductive health.

Zinc picolinate supports skin hormone balance and immune system health.

Viatrona^TM – First Targeted Nutrient Replenishment for Women on Hormonal Contraceptives

Other Nutrients at Risk

Hormonal contraceptives don’t just deplete the B vitamins and magnesium—they can also chip away at several other essential nutrients over time:

• Selenium – Supports thyroid hormone metabolism and acts as a powerful antioxidant to combat cellular stress. Deficiency may worsen fatigue and mood swings.
• Vitamin C – Crucial for collagen synthesis, immune defence, and regulating cortisol. Depletion can impair skin health and increase oxidative stress.
• Vitamin E – Plays a vital role in fertility, cellular protection, and reducing inflammation caused by hormonal shifts or synthetic hormones.
• Vitamin B2 (Riboflavin) – Supports energy production, liver detox pathways, and helps activate other B vitamins.
• Vitamin D – While not directly depleted by the pill, studies show that women on hormonal contraception often have lower serum vitamin D levels, which can impact immunity, bone health, and mood balance.

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Hormonal birth control can affect gut integrity, disrupt the microbiome, and increase demand on liver methylation and detox enzymes—all of which influence how well your body absorbs and uses nutrients.

Nutritional Deficiencies, Blood Clots, and Methylation

You may be aware of the link between hormonal contraceptives and an increased risk of blood clots, but it is less well known that nutrient deficiencies may play a hidden role in this process.

Folate, vitamin B6 and vitamin B12 play a key role in the methylation cycle, which is responsible for converting homocysteine (a pro-inflammatory amino acid) into harmless by-products. A deficiency in any of these nutrients can cause homocysteine levels to rise. Elevated homocysteine levels are associated with endothelial damage, increased blood clot formation, and the risk of cardiovascular disease.

🩸 Hormonal contraceptives and blood clotting:

Oestrogen-containing contraceptives (such as combined pills) already increase the risk of thrombosis by altering the balance of blood clotting factors. When combined with nutrient deficiencies, especially folic acid and vitamin B6, the risk can be exacerbated. In other words, the body becomes more prone to blood clots and less able to control homocysteine levels.

The active form of folate (L-5-MTHF) and vitamin B6 (P-5-P) help convert homocysteine into less harmful compounds. Without sufficient levels of these substances, this process slows down, raising concerns not only for cardiovascular health, but also for brain function, mood regulation and fertility.

A deficiency in folic acid and vitamin B6 may increase the risk of blood clots, especially when using hormonal contraceptives.

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How to Rebuild — Without Too Many Different Bottles

In an attempt to restore nutrient reserves while taking birth control, many women may find themselves taking a variety of supplements. Often, women end up taking 5–10 different supplements, which often contain repetitive or poorly absorbed ingredients.

That's why I created a 2-capsule solution combined with an oil supplement, designed for maximum bioavailability and nutrient synergy. It's a simplified, science-based approach to replenishing what pills quietly deplete: B vitamins, magnesium, zinc, selenium, antioxidants, and more.

🟣 Why it matters: We don't need a lot of different supplements; we need one smart combination. Fewer steps. Better absorption. A regimen that respects your time, your finances, and your body.

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Who Should Supplement While on the Pill?

• Long-term users
• Women with mood, skin, fatigue, or libido concerns
• Athletes and high-stress individuals
• Preconception or fertility planning
• Anyone coming off hormonal birth control

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How to Test for Deficiencies

Symptoms such as fatigue, anxiety, hair loss or poor sleep may indicate a deficiency, but laboratory tests provide more accurate information. Functional medicine goes beyond basic tests.

Key markers include B12 (active and methylmalonic acid), magnesium in red blood cells, homocysteine, folate, and zinc in serum. For a deeper understanding, consider testing for organic acids in urine or MTHFR variants, which affect how your body absorbs B vitamins. These markers will help identify what exactly contraceptives may be depleting without you noticing.

🟣 Track and repeat testing every 6 months. Pay attention to changes in symptoms, increased energy, and restoration of nutrient levels — not just ‘normal’ levels, but optimal levels.

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What Supplements Should I Take on the Pill?

• Focus on activated, bioavailable, and multi-nutrient formulas
• Benefits of choosing forms like:
  • P5P (B6)
  • Methyl-B12
  • L-5-MTHF
  • Magnesium glycinate
  • Zinc picolinate

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Additional Reading & Resources

What the FDA Has (and Hasn’t) Said

While the FDA mandates that drug manufacturers disclose known side effects, nutritional depletion is often underemphasized. However, the FDA-approved labelling for oral contraceptives does acknowledge that estrogen-containing birth control can reduce levels of folate, vitamin B6, and B12—nutrients essential for mood, energy, and methylation. Some brands even include folate to mitigate this. Despite these warnings, many healthcare providers overlook nutrient monitoring during long-term contraceptive use. Functional medicine flags this gap, advocating for proactive testing and replenishment—especially in women with mood issues, fatigue, or plans for pregnancy.

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Synthetic Dyes and Estrogenic Additives in Medications

Many hormonal contraceptives—and other common medications—contain synthetic dyes like FD&C Red #40 or Yellow #6, which have been flagged for potential estrogenic activity and gut-disrupting effects. These additives are used for appearance, not function, yet can burden the liver and hormone pathways, especially in sensitive individuals. Functional medicine practitioners raise concerns about cumulative exposure to xenoestrogens, especially in women already dealing with hormonal imbalances.

🟣 Smart swap: Choosing cleaner formulations, supporting detox pathways, and replenishing depleted nutrients helps counteract these hidden stressors—and supports real hormonal resilience.

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Hormonal Birth Control and Gut Barrier Integrity

Emerging research shows that oral contraceptives may compromise gut barrier function, contributing to increased intestinal permeability, often called “leaky gut.” Synthetic estrogens and progestins can alter gut microbiota, reduce microbial diversity, and weaken tight junctions in the intestinal lining. This disruption may lead to inflammation, bloating, food sensitivities, and poor nutrient absorption. In functional medicine, gut health is central to hormone balance, immune regulation, and mood.

🟣 Support your gut: Replenish nutrients, add targeted probiotics, and use gut-repairing compounds like L-glutamine, zinc carnosine, and quercetin to protect your inner barrier.

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