10 Causes of Nutrient Deficiencies

Why Nutrient Deficiencies Happen - Even With a “Healthy” Diet

I’m a big believer in getting most of our nutrients from food. Whole foods contain a synergistic blend of vitamins, minerals, and phytochemicals that generally improve how nutrients are absorbed and used by the body.

But even with a healthy diet, there are many reasons we may still fall short on key nutrients - and over time, that can lead to deficiencies.

10 Causes of Nutrient Deficiencies

1. A highly processed diet

One of the most obvious reasons for nutrient deficiencies is simply not eating enough nutrient-dense food. The Standard American Diet is heavy in packaged, processed, and fast foods, which are often low in essential nutrients. On top of that, processed foods can place extra demands on the body because it uses nutrients to metabolize excess sugar, unhealthy fats, additives, and preservatives. Many also contain poor-quality oils that can promote inflammation.

2. Poor soil quality

Even a great diet may not provide what it once did. Modern farming practices have depleted many soils of key minerals, which can mean our food is less nutrient-rich than it used to be. Choosing organic can help, since organic foods are often grown in better soil and reduce pesticide exposure, which may also affect gut health and nutrient absorption.

3. Low stomach acid or digestive issues

Stomach acid is essential for breaking down food so nutrients can be absorbed. Low stomach acid - which can become more common with age and with the use of antacids or PPIs - may impair digestion and absorption. Other gut issues, including food intolerances, bacterial overgrowth, infections, or inflammation, can also interfere with nutrient uptake.

4. Anti-nutrients

Some foods contain natural compounds that can reduce mineral absorption. For example, phytic acid in grains, nuts, legumes, and soy can bind to minerals like zinc and magnesium. Traditional preparation methods such as soaking, sprouting, and fermenting can often reduce these compounds and improve absorption.

5. Missing key co-factors

Nutrients don’t work in isolation. Many require other nutrients to be properly absorbed and utilized. Calcium, for example, depends on vitamin D, magnesium, vitamin K, and trace minerals to help direct it into bone. Without those co-factors, the calcium is not effectively absorbed into bone. For example, milk contains calcium, but is missing many of the key co-factors, whereas cheese and yogurt contain more of the co-factors - which is probably why milk is poorly correlated with bone health, while cheese and yogurt are. This is true for supplements as well - high quality supplements will contain key co-factors for absorption & utlization.

6. Prescription medications

Many medications can deplete vitamins, minerals, and other nutrients. This is one reason it is important to review both medications and nutritional status together, especially when symptoms of deficiency are present.

7. Avoiding food groups

Whether due to allergies, intolerances, ethics, religion, or personal preference, avoiding certain food groups can increase the risk of missing key nutrients. For example, vitamin B12 is found primarily in animal foods, so those following a vegan diet typically need to supplement it.

8. Genetic factors

Genetics can affect how well we process and use certain nutrients. Some people have reduced ability to convert nutrients into their active forms, which can increase their risk of deficiency. One common example involves methylation-related gene variants, which may affect the metabolism of folate and vitamin B12.

9. Low-fat diets or fat absorption issues

Fat-soluble vitamins (A, D, E, and K) require fat for proper absorption. So extremely low fat diets may impair absorption of these nutrients. People with gallbladder issues or impaired fat digestion may also struggle to absorb fat-soluble nutrients.

10. Lack of sun exposure

Vitamin D is one of the most common deficiencies, in part because sunlight is our primary source. Spending most of our time indoors, covering up, or using sunscreen all the time can reduce vitamin D production in the skin.

How can you tell if you have a deficiency?

Sometimes there are no obvious symptoms. Other times, nutrient deficiencies can show up as fatigue, headaches, dry skin, low mood, numbness or tingling, poor focus, lowered immunity, appetite changes, loss of taste or smell, or unexplained changes in weight.

In some cases, deficiencies can become severe enough to mimic other conditions. That’s why testing can be useful when symptoms are persistent or unclear.

If you suspect a deficiency, targeted testing can help identify what’s actually low so supplementation can be more precise.

Do you need supplements long term?

Not always.

Some supplements are helpful short term, during periods of stress, illness, recovery, or when addressing a specific issue. Others may be beneficial long term to support general health or fill common nutritional gaps.

The goal is not to replace food with supplements. It’s to use supplements strategically, when needed, to support the body.

The top 3 supplements almost everyone can benefit from

1. Magnesium

Magnesium is involved in hundreds of enzymatic reactions in the body, including energy production, muscle and nerve function, blood sugar regulation, bone health, and stress resilience. Low magnesium can contribute to muscle cramps, headaches, poor sleep, constipation, and heart rhythm issues.

Food sources include leafy greens, pumpkin seeds, beans, avocado, and cacao.

If supplementing, forms such as glycinate, malate, citrate, and orotate are often preferred over magnesium oxide, which is poorly absorbed and more likely to act as a laxative.

2. Vitamin D

Vitamin D functions more like a hormone than a vitamin and plays a critical role in immune health, bone strength, mood, and metabolic function. Low levels are common, especially in people with limited sun exposure.

Sunlight is the best source, but supplementation may be appropriate for some people. If supplementing, vitamin D3 is generally preferred over D2. Because vitamin D works closely with magnesium, it often makes sense to think about both together.

Ideally, vitamin D levels should be tested periodically so dosing can be individualized.

3. B vitamins

B vitamins are essential for converting food into energy and supporting the nervous system, mood, detoxification, and metabolism. Because they are water-soluble and stress increases demand for them, low levels are common.

B vitamins are ideally taken together as a full B complex, but some individuals may benefit from higher doses of individual B vitamins. The B vitamins are comprised of:

• B12 for energy, nerve health, memory, and red blood cell production

• B6 for neurotransmitters, hormone balance, and metabolism

• Folate (B9) for methylation, homocysteine balance, and fetal development

• B1 (thiamine) for carbohydrate metabolism, nerve function, and energy

• B2 (riboflavin) for energy production and migraine support

• Biotin (B7) for hair, skin, and nails

Focus on Foods

Food should always be the foundation. But because of modern diets, depleted soils, digestive issues, medications, stress, genetics, and lifestyle factors, supplements can still play an important role.

That said, more is not always better. Some nutrients can accumulate in the body, and poor-quality supplements may be ineffective — or even counterproductive.

So if you choose to supplement, focus on quality, appropriate dosing, and the right co-factors. And remember: supplements are meant to supplement a healthy diet, not replace one.

A note about where you buy supplements

Quality matters when it comes to supplements. Unlike prescription medications, supplements are not tightly regulated, and quality can vary significantly between brands.

For that reason, I always recommend purchasing supplements from reputable companies that test for purity, potency, and contaminants.

Be cautious when buying supplements from large online marketplaces like Amazon. While many legitimate brands are sold there, products are often distributed through third-party sellers, which can increase the risk of counterfeit, expired, or improperly stored products.

Whenever possible, purchase supplements directly from the manufacturer or through a trusted practitioner dispensary, where the supply chain is controlled and the products are more likely to be authentic.

You can obtain quality practitioner grade supplements on Fullscript:

Before starting new supplements, those taking prescription medications or who have an existing health condition should consult with their doctor first to make sure there are no interactions or contraindications.