7 Nutrient Deficiencies That Make Hashimoto’s Symptoms Worse

Hashimoto’s doesn’t just affect your thyroid.

It impacts your ability to absorb nutrients, which can make almost every single one of your symptoms worse.

Here’s how:

Hashimoto’s is an autoimmune disease that causes chronic inflammation. That inflammation negatively impacts your stomach and your gut.

When this happens, your body starts to spill out the very nutrients you need to feel better.

If you’ve ever felt like your treatment isn’t working as well as it should, there’s a good chance one or more of these deficiencies is involved.

#1. Vitamin B12

One of the most overlooked connections in Hashimoto’s is with B12.

You already know Hashimoto’s is an autoimmune disease. What you may not know is that when you have one autoimmune disease, you are much more likely to get others.

There are several that cluster with Hashimoto’s, but one of the most common is called atrophic gastritis.

If you have this condition, your immune system attacks your stomach, killing off the cells that produce an enzyme called intrinsic factor, which your body requires to absorb vitamin B12.

In short:

Hashimoto’s → increased autoimmune activity → atrophic gastritis → poor B12 absorption → B12 deficiency.^[1]

This is a problem all on its own, but it gets worse when you realize just how much of an overlap there exists between the symptoms of hypothyroidism and B12 deficiency:

Fatigue, brain fog, depression, anxiety, and irritability.

Having both means makes diagnosing and treating the other very difficult.

The good news is that the solution is simple:

Take 1,000 mcg of methylcobalamin, adenosylcobalamin, and hydroxycobalamin together.

This combination and dose is enough to bypass any issues related to intrinsic factor, methylated defects, and absorption.

It brute forces the B12 you need into your body and cells.

#2. Selenium

Your thyroid gland has the highest selenium concentration per gram of tissue of any organ in your body.

It needs selenium to make thyroid hormones and to protect itself from the oxidative damage that Hashimoto’s inflammation constantly creates.

When selenium is low, thyroid gland inflammation goes up, antibody levels rise, free T3 drops, and reverse T3 climbs.

Research backs this up:

Selenium supplementation consistently reduces TPO antibodies in Hashimoto’s patients, often by 40% or more.^[2]

How to fix it: Take 75-200 mcg daily as selenomethionine or selenium glycinate complex.

For even better results, combine selenium with zinc. Selenium provides protection to your thyroid, while zinc helps your body create more T3.

These two minerals go hand in hand.

Give both of them 8-12 weeks to take effect and to see changes in your symptoms and antibody levels.

#3. Zinc

Zinc plays an important role in the conversion of T4 to T3 and in how T3 interacts with the thyroid nuclear receptor.

Without enough zinc in your body, the nuclear receptor can’t take on the correct shape, which impacts T3’s ability to bind to it.

Practically speaking, this means that you can have normal T3 levels when you look at your labs, but still feel hypothyroid. ^[3]

Signs that you don’t have enough zinc include: hair loss, slow metabolism, low free T3, and poor immune function.

A semi-reliable (but non-specific) way to qualitatively assess your zinc status is by asking yourself this question:

Am I always getting sick?

If so, zinc is one of the first things you should look for because of its impact on your immune system.

The relationship between your thyroid and zinc is considered bidirectional. That is, as thyroid hormone levels drop, it causes your body to lose zinc, which then makes your thyroid even worse, and the cycle continues.

If you think you don’t have enough zinc in your body, here’s how to fix it:

Take 5-15 mg daily as zinc citrate or zinc glycinate.

Some providers recommend zinc picolinate; I do not. Research shows that it’s no better than the other forms, and it may bind so tightly that your body can’t use the zinc it carries.

For best results, take lower doses, but use them more frequently and always remember to take zinc with food to prevent stomach upset.

Like selenium, allow 8-12 weeks for it to take effect in your body.

#4. Magnesium

Magnesium deficiency may be one of the most common (and underappreciated) nutrient deficiencies for Hashimoto’s patients.

It’s tricky for a few reasons:

• Hashimoto’s causes chronic stress, and stress is a known depletor of magnesium levels. The more stressed your system is, the more magnesium you burn through.
• Thyroid dysfunction may accelerate the elimination of magnesium through the kidneys.
• Research shows that very low magnesium levels are associated with higher rates of Hashimoto’s, suggesting there may be a causal relationship. ^[4]
• The foods that are naturally highest in magnesium are the foods that patients with Hashimoto’s don’t get enough of: green vegetables.

For these reasons, magnesium is not one of those nutrients you can take for a few weeks and then stop. It’s going to be something you always need to come back to.

When you’re low, you’ll feel it as constipation, muscle cramps, anxiety, poor sleep, and increased sensitivity to stress.

How to fix it: Take 100-300 mg of magnesium daily.

But the form and dose that you take matter. For Hashimoto’s, these work best:

• Magnesium O7 (ozonated) for constipation
• Magnesium glycinate for sleep and anxiety
• Sucrosomial magnesium for thyroid, muscle, and sleep support

#5. Iron

Your thyroid requires iron to create T4 and T3.

The enzyme thyroid peroxidase is what we call “heme-dependent” or “iron-dependent”.

When iron is low, that enzyme becomes less active, and your thyroid hormone production drops.^[5]

The symptoms of low iron are hard to miss, but they can be confused with other things.

The most common include: extreme fatigue, hair loss, shortness of breath, and low T4 and T3.

What makes iron deficiency especially common in Hashimoto’s is two-fold:

First, chronic gut inflammation impairs its absorption.

And second, Hashimoto’s primarily impacts women, who are constantly losing iron from their menstrual cycle.

But before you ever take an iron supplement, you must check your levels.

The best way to do that is by looking at a value called ferritin, not just serum iron.

If your ferritin is below 60 ng/mL, that’s a problem that needs to be corrected.

Bottom line:

Semi-regularly, make sure to check your iron and ferritin along with your thyroid labs.

If your ferritin is below 60, supplement with iron or increase red meat consumption.

But remember: never supplement with iron without testing.

Taking too much can actually worsen Hashimoto’s inflammation.

#6. Iodine

Iodine is a point of confusion among many Hashimoto’s patients because they’ve been told to avoid it 100%.

But that’s not correct advice.

Your thyroid cannot make any hormone without iodine. Period.

Let me repeat, you cannot live without iodine. You MUST get it from somewhere.

The problem is all about the dose.

Take too much, and you definitely can make Hashimoto’s worse. Research has shown that iodine can accelerate the autoimmune attack on your thyroid gland by making thyroglobulin more immunogenic. ^[6]

But if you avoid it, you can also make your thyroid function worse.

The solution is to take just the right amount.

And that sweet spot is around 200-300 mcg per day, from all sources combined.

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That includes food sources of iodine like milk, eggs, strawberries, and iodized salt.

As well as cosmetics like shampoos and makeup.

Most patients with Hashimoto’s have no idea where iodine is hiding or how much they are actually getting.

And many of the same people who try to avoid it in supplements are getting overdosed by their food and cosmetics without even realizing it.

Here’s how I recommend addressing iodine supplements:

First, don’t ever supplement with high-dose iodine. Anything above 1 gram per day is generally not a good idea.

If you do decide you need to supplement, keep it low and always pair it with selenium.

These guidelines will keep your thyroid safe.

#7. Vitamin D

I don’t think I’ve ever seen a patient with Hashimoto’s who wasn’t deficient in vitamin D.

The only exception are those who are already supplementing.

The reality is, most people just aren’t consuming the right foods or staying in the sun long enough to get optimal levels.

And that’s a problem because vitamin D functions more like a hormone than a vitamin.

It plays a direct role in regulating your immune system, which means low vitamin D can exacerbate and accelerate the attack on your thyroid gland.

Research shows vitamin D deficiency correlates strongly with higher TPO and anti-TG antibody levels, and that correcting it can cause these antibodies to drop.^[7]

The symptoms of vitamin D deficiency are easy to confuse with hypothyroidism and include hair thinning, slow hair growth, fatigue, depression, and muscle weakness.

My advice is this:

Regularly check your 25-hydroxy vitamin D levels when you get your thyroid labs.

If you’re low, take 2,000-5,000 IU of D3 daily, always paired with K2 and vitamin A.

For best results, take it with a fatty meal to ensure absorption.

Match Your Symptoms to the Right Deficiency

Don’t stress about trying to fix all of these at once.

Instead, look at what’s bothering you the most.

If brain fog and anxiety are your biggest issues, start with B12 and magnesium.

If hair loss is a problem for you, check your zinc and iron.

If your antibodies are high and you want to bring them down, try selenium and vitamin D.

And if you like the idea of getting as many vitamins from your food as possible, make sure you check out this article next.

Scientific References

1. Kacharava, T., Tkemaladze, T., Giorgadze, E., Ubiria, I., & Asanidze, M. (2023). Correlation Between Vitamin B12 Deficiency and Autoimmune Thyroid Diseases. Endocrine, Metabolic & Immune Disorders – Drug Targets, 23(1), 86-94. [https://doi.org/10.2174/1871530322666220627145635]
2. Huwiler, V.V., et al. (2024). Selenium supplementation in patients with Hashimoto thyroiditis: a systematic review and meta-analysis of randomized clinical trials. Thyroid. [https://doi.org/10.1089/thy.2023.0556]
3. Severo, J.S., Morais, J.B.S., de Freitas, T.E.C., Andrade, A.L.P., Feitosa, M.M., Fontenelle, L.C., de Oliveira, A.R.S., Cruz, K.J.C., & Marreiro, D.N. (2019). The Role of Zinc in Thyroid Hormones Metabolism. International Journal for Vitamin and Nutrition Research, 89(1-2), 80-88. [https://doi.org/10.1024/0300-9831/a000262]
4. Wang, K., Wei, H., Zhang, W., Li, Z., Ding, L., Yu, T., Tan, L., Liu, Y., Liu, T., Wang, H., Fan, Y., Zhang, P., Shan, Z., & Zhu, M. (2018). Severely low serum magnesium is associated with increased risks of positive anti-thyroglobulin antibody and hypothyroidism: A cross-sectional study. Scientific Reports, 8(1), 9904. [https://doi.org/10.1038/s41598-018-28362-5]
5. Garofalo, V., Condorelli, R.A., Cannarella, R., Aversa, A., Calogero, A.E., & La Vignera, S. (2023). Relationship between Iron Deficiency and Thyroid Function: A Systematic Review and Meta-Analysis. Nutrients, 15(22), 4790. [https://doi.org/10.3390/nu15224790]
6. Hu, S., & Rayman, M.P. (2017). Multiple Nutritional Factors and the Risk of Hashimoto’s Thyroiditis. Thyroid. [https://doi.org/10.1089/thy.2016.0635]
7. Jiang, X., Huang, J., Wang, Y., & Gao, W. (2022). Effects of vitamin D treatment on thyroid function and autoimmunity markers in patients with Hashimoto’s thyroiditis: A meta-analysis of randomized controlled trials. Journal of Clinical Pharmacy and Therapeutics, 47, 767-775. [https://doi.org/10.1111/jcpt.13605]